purlGTN:N00063 |
News |
Feedback: Easy slide recordings feedbacktestimonialgtn |
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purlGTN:N00062 |
News |
GTN has left Twitter/X as of October gtncommunications |
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purlGTN:N00061 |
News |
Update: Workflow List now searches WorkflowHub.eu, advanced query syntax feature updategtn |
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purlGTN:N00060 |
News |
Single cell subdomain re-launch: Unified and feedback-driven gtnsinglecell |
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purlGTN:N00059 |
News |
New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets new featuregtn |
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purlGTN:N00058 |
News |
New Feature: GTN User Preferences new featuregtn |
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purlGTN:N00057 |
News |
AI4Life teams up with GTN to enhance training resources new topicnew community |
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purlGTN:N00056 |
News |
ELIXIR-UK Fellow Launches New FAIR Data Management Training new topicnew tutorial |
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purlGTN:N00055 |
News |
New Feature: Pan-Galactic Tool Search new featuregtn |
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purlGTN:N00054 |
News |
GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis
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purlGTN:N00053 |
News |
New Galaxy training: Genome-wide alternative splicing analysis new tutorial |
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purlGTN:N00052 |
News |
BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More new topicnew feature |
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purlGTN:N00051 |
News |
New Feature: my.galaxy.training new featuregtn |
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purlGTN:N00050 |
News |
New Feature: Persistent URLs (PURLs) / Shortlinks new featuregtn |
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purlGTN:N00049 |
News |
New Feature: GTN Rdoc new featuregtn |
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purlGTN:N00048 |
News |
New Feature: Click-to-run Workflows new featuregtn |
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purlGTN:N00047 |
News |
New Feature: Learning Pathways! new feature |
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purlGTN:N00046 |
News |
New Feature: Trainer Directory! (Add yourself today!) new featurecommunity buildingcapacity building |
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purlGTN:N00045 |
News |
What are the most used tools in the GTN? new featuregtn |
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purlGTN:N00044 |
News |
GTN Celebrates Black History Month
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purlGTN:N00043 |
News |
New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition new tutorial |
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purlGTN:N00042 |
News |
New Feature: Prometheus Metrics endpoint new featuregtn |
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purlGTN:N00041 |
News |
New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic new topicnew feature |
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purlGTN:N00040 |
News |
New GTN paper: "Galaxy Training: A powerful framework for teaching!" paper |
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purlGTN:N00039 |
News |
New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation! new tutorialsingle-celltranscriptomics |
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purlGTN:N00038 |
News |
New Topic: Single Cell Analysis! new topicsingle-cellnew feature |
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purlGTN:N00037 |
News |
New Tutorial: Data Manipulation new tutorial |
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purlGTN:N00036 |
News |
New Tutorial: Workflow Reports new tutorialGalaxy Tips & Tricks |
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purlGTN:N00035 |
News |
GTN Metadata Schemas new feature |
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purlGTN:N00034 |
News |
New Tutorial Feature: Choose Your Own Tutorial gtn infrastructurenew featuretutorial authors |
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purlGTN:N00033 |
News |
New Tutorial: VGP assembly pipeline new tutorialassemblypacbiovgp |
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purlGTN:N00032 |
News |
New Feature: Automatic RMarkdown gtn infrastructurenew feature |
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purlGTN:N00031 |
News |
GTN Smörgåsbord 2: Tapas Edition event |
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purlGTN:N00030 |
News |
Support for annotating Funding Agencies new-feature |
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purlGTN:N00029 |
News |
New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate new tutorialassemblygenome-annotation |
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purlGTN:N00028 |
News |
New FAQs: How does the GTN stay FAIR and Collaborative faq |
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purlGTN:N00027 |
News |
New Feature: GTN Video Library gtn infrastructurenew feature |
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purlGTN:N00026 |
News |
New Feature: GTN API with OpenAPI 3 specification gtn infrastructurenew feature |
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purlGTN:N00025 |
News |
Attention Contributors: GTN Performance Enhancements authorsdevelopersperformance |
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purlGTN:N00024 |
News |
New Topic: Data Science Survival Kit gtn infrastructurenew topic |
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purlGTN:N00023 |
News |
Got a minute? Take our survey about Galaxy for training and have your say! feedback |
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purlGTN:N00022 |
News |
New Feature: Automatic Jupyter Notebooks gtn infrastructurenew feature |
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purlGTN:N00021 |
News |
New Feature: a feedback page to aggregate and display feedback answers new featurecontributors |
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purlGTN:N00020 |
News |
Accessibility Improvements new feature |
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purlGTN:N00019 |
News |
New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data new tutorialvariant-analysiscovid-19 |
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purlGTN:N00018 |
News |
New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R new tutorialvisualization |
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purlGTN:N00017 |
News |
New Tutorial: GitPod for contributing to the GTN new tutorialcontributors |
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purlGTN:N00016 |
News |
New Tutorial: Genome Annotation with Apollo new tutorialgenome-annotation |
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purlGTN:N00015 |
News |
Oh no, it changed! Quick, to the archive menu. new feature |
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purlGTN:N00014 |
News |
Contributing to BioBlend as a developer new tutorial |
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purlGTN:N00013 |
News |
New Feature: Easy Abbreviation new feature |
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purlGTN:N00012 |
News |
¿Hablas español?: The first curated tutorial in Spanish! new tutorialespañol |
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purlGTN:N00011 |
News |
New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana new tutorialtranscriptomicsplantsmirna |
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purlGTN:N00010 |
News |
New Feature: Video Player gtn infrastructurevideonew feature |
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purlGTN:N00009 |
News |
New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy new tutorialsingle-cellplant |
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purlGTN:N00008 |
News |
New Tutorials: Genome assembly of a MRSA genome new tutorialassemblymrsaamrnanoporeillumina |
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purlGTN:N00007 |
News |
New Feature: FAQs gtn infrastructurecontributorsinstructorsnew feature |
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purlGTN:N00006 |
News |
New Tutorial: Object tracking using CellProfiler new tutorialimaging |
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purlGTN:N00005 |
News |
Next GTN CoFest May 20, 2021 cofest |
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purlGTN:N00004 |
News |
Galaxy Community Conference 2021 event |
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purlGTN:N00003 |
News |
Report on the GTN Smörgåsbord event eventpandemicremote-teaching |
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purlGTN:N00002 |
News |
Galaxy 21.01 released! galaxy |
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purlGTN:N00001 |
News |
New Feature: Automatic Slides-to-video conversion new featurevideosgtnpandemicremote-teaching |
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purlGTN:N00000 |
News |
Galaxy Admin Training Success admingateventpandemicremote-teaching |
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purlGTN:F00282 |
FAQs |
Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?
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Proteomics |
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purlGTN:F00283 |
FAQs |
Including custom modifications into MaxQuant in Galaxy?
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Proteomics |
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purlGTN:F00284 |
FAQs |
Which isobaric labeled quantification methods does MaxQuant in Galaxy support?
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Proteomics |
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purlGTN:F00137 |
FAQs |
How does the GTN ensure accessibility?
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purlGTN:F00002 |
FAQs |
How do I create an account on a public Galaxy instance?
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purlGTN:F00253 |
FAQs |
It says I already have an account when registering for ecology.usegalaxy.eu
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Ecology |
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purlGTN:F00003 |
FAQs |
Can I create multiple Galaxy accounts?
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purlGTN:F00004 |
FAQs |
How can I reduce quota usage while still retaining prior work (data, tools, methods)?
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purlGTN:F00005 |
FAQs |
How to update account preferences?
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purlGTN:F00254 |
FAQs |
Automatically trim adapters (without providing custom sequences)
|
Epigenetics |
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purlGTN:F00274 |
FAQs |
How can I adapt this tutorial to my own data?
|
Metagenomics |
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purlGTN:F00271 |
FAQs |
How can I adapt this tutorial to my own data?
|
Metagenomics |
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purlGTN:F00184 |
FAQs |
Operating system compatibility
|
Galaxy Server administration |
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purlGTN:P00000 |
|
Admin Training Course Galaxy administrators5-day course |
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purlGTN:F00280 |
FAQs |
What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?
|
Proteomics |
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purlGTN:F00321 |
FAQs |
Why is Alevin is not working?
|
Single Cell |
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purlGTN:F00320 |
FAQs |
Why is Alevin is not working?
|
Single Cell |
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purlGTN:F00306 |
FAQs |
Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?
|
Proteomics |
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purlGTN:F00234 |
FAQs |
Is it possible to use alternative tools to those proposed in the tutorial?
|
Assembly |
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purlGTN:F00225 |
FAQs |
Why is amplification more of an issue in scRNA-seq than RNA-seq?
|
Single Cell |
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purlGTN:F00006 |
FAQs |
Adding a custom database/build (dbkey)
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purlGTN:F00174 |
FAQs |
Pick the right Concatenate tool
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purlGTN:F00007 |
FAQs |
Beware of Cuts
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purlGTN:F00008 |
FAQs |
Extended Help for Differential Expression Analysis Tools
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purlGTN:F00009 |
FAQs |
Will my jobs keep running?
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purlGTN:F00010 |
FAQs |
My jobs aren't running!
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purlGTN:F00011 |
FAQs |
Regular Expressions 101
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purlGTN:F00012 |
FAQs |
Reporting usage problems, security issues, and bugs
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purlGTN:F00013 |
FAQs |
Results may vary
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purlGTN:F00014 |
FAQs |
Troubleshooting errors
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purlGTN:F00015 |
FAQs |
What information should I include when reporting a problem?
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purlGTN:F00216 |
FAQs |
I can’t find the “Analyze Data” button
|
Introduction to Galaxy Analyses |
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purlGTN:F00325 |
FAQs |
AnnData Import/ AnnData Manipulate not working?
|
Single Cell |
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purlGTN:F00185 |
FAQs |
Variable connection
|
Galaxy Server administration |
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purlGTN:F00186 |
FAQs |
Define once, reference many times
|
Galaxy Server administration |
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purlGTN:F00187 |
FAQs |
What if you forget `--diff`?
|
Galaxy Server administration |
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purlGTN:F00188 |
FAQs |
Error: "skipping: no hosts matched"
|
Galaxy Server administration |
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purlGTN:F00189 |
FAQs |
Running Ansible on your remote machine
|
Galaxy Server administration |
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purlGTN:F00190 |
FAQs |
What is the difference between the roles with `role:` prefix and without?
|
Galaxy Server administration |
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purlGTN:F00191 |
FAQs |
How do I know what I can do with a role? What variables are available?
|
Galaxy Server administration |
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purlGTN:F00192 |
FAQs |
How do I see what variables are set for a host?
|
Galaxy Server administration |
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purlGTN:F00193 |
FAQs |
Is YAML sensitive to True/true/False/false
|
Galaxy Server administration |
|
|
purlGTN:F00236 |
FAQs |
Why does my assembly graph in Bandage look different to the one pictured in the tutorial?
|
Assembly |
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|
purlGTN:F00243 |
FAQs |
The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
|
Development in Galaxy |
|
|
purlGTN:F00255 |
FAQs |
In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?
|
Epigenetics |
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|
purlGTN:F00285 |
FAQs |
What is the advantage of breaking down protein to peptides before mass spec?
|
Proteomics |
|
|
purlGTN:F00277 |
FAQs |
The Build tissue-specific expression dataset tool (step one) exits with an error code.
|
Proteomics |
|
|
purlGTN:F00194 |
FAQs |
Opening a split screen in byobu
|
Galaxy Server administration |
|
|
purlGTN:F00307 |
FAQs |
Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
|
Proteomics |
|
|
purlGTN:P00001 |
|
Discovering galaxy through climate analysis ClimateOverview |
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purlGTN:F00259 |
FAQs |
Do you have resources to help me get started working in the cloud?
|
Using Galaxy and Managing your Data |
|
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purlGTN:F00138 |
FAQs |
How does the GTN implement the "Ten simple rules for collaborative lesson development"
|
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purlGTN:F00016 |
FAQs |
Adding a tag to a collection
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purlGTN:F00017 |
FAQs |
Creating a dataset collection
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purlGTN:F00018 |
FAQs |
Creating a paired collection
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purlGTN:F00182 |
FAQs |
Changing the datatype of a collection
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purlGTN:F00183 |
FAQs |
Converting the datatype of a collection
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purlGTN:F00019 |
FAQs |
Renaming a collection
|
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purlGTN:F00245 |
FAQs |
I want to use a collection for outputs but it always passes the test even when the script fails. Why?
|
Development in Galaxy |
|
|
purlGTN:F00296 |
FAQs |
How does one compare metaproteomics measurements from two experimental conditions?
|
Proteomics |
|
|
purlGTN:F00341 |
FAQs |
After sequencing with MinKNOW software, we get many fastq files, do these files need to be combined into one file before uploading or is it possible to upload them all at once?
|
Metagenomics |
|
|
purlGTN:F00286 |
FAQs |
Do we need a contaminant FASTA for MQ in galaxy?
|
Proteomics |
|
|
purlGTN:F00214 |
FAQs |
How to Contribute to Galaxy
|
Development in Galaxy |
|
|
purlGTN:F00212 |
FAQs |
Contributing a Jupyter Notebook to the GTN
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00139 |
FAQs |
Thanks!
|
|
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|
purlGTN:F00140 |
FAQs |
How can I get started with contributing?
|
|
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|
purlGTN:F00141 |
FAQs |
How can I contribute in "advanced" mode?
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|
purlGTN:F00142 |
FAQs |
How can I fix mistakes or expand an existing tutorial using the GitHub interface?
|
|
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|
purlGTN:F00143 |
FAQs |
How can I give feedback?
|
|
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|
purlGTN:F00144 |
FAQs |
What can I do to help the project?
|
|
|
|
purlGTN:F00145 |
FAQs |
How can I report mistakes or errors?
|
|
|
|
purlGTN:F00146 |
FAQs |
How can I test an Interactive Tour?
|
|
|
|
purlGTN:F00147 |
FAQs |
How can I create new content without dealing with git?
|
|
|
|
purlGTN:F00297 |
FAQs |
How does one convert RAW files to MGF peak lists within Galaxy?
|
Proteomics |
|
|
purlGTN:F00298 |
FAQs |
I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?
|
Proteomics |
|
|
purlGTN:F00233 |
FAQs |
Customising the welcome page
|
Galaxy Server administration |
|
|
purlGTN:F00195 |
FAQs |
Database Issues
|
Galaxy Server administration |
|
|
purlGTN:F00020 |
FAQs |
Incomplete Dataset Download
|
|
|
|
purlGTN:F00021 |
FAQs |
How to find and correct tool errors related to Metadata?
|
|
|
|
purlGTN:F00023 |
FAQs |
Finding BAM dataset identifiers
|
|
|
|
purlGTN:F00024 |
FAQs |
Directly obtaining UCSC sourced *genome* identifiers
|
|
|
|
purlGTN:F00025 |
FAQs |
Adding a tag
|
|
|
|
purlGTN:F00177 |
FAQs |
Changer le type de données
|
|
|
|
purlGTN:F00026 |
FAQs |
Changing the datatype
|
|
|
|
purlGTN:F00128 |
FAQs |
Cambiar el tipo de datos
|
|
|
|
purlGTN:F00027 |
FAQs |
Changing database/build (dbkey)
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|
|
|
purlGTN:F00028 |
FAQs |
Mismatched Chromosome identifiers and how to avoid them
|
|
|
|
purlGTN:F00029 |
FAQs |
Converting the file format
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|
|
|
purlGTN:F00030 |
FAQs |
Creating a new file
|
|
|
|
purlGTN:F00031 |
FAQs |
How to set Data Privacy Features?
|
|
|
|
purlGTN:F00032 |
FAQs |
Detecting the datatype (file format)
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|
|
|
purlGTN:F00033 |
FAQs |
Downloading datasets
|
|
|
|
purlGTN:F00034 |
FAQs |
Downloading datasets using command line
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|
|
|
purlGTN:F00035 |
FAQs |
Finding Datasets
|
|
|
|
purlGTN:F00036 |
FAQs |
How to unhide "hidden datasets"?
|
|
|
|
purlGTN:F00037 |
FAQs |
Different dataset icons and their usage
|
|
|
|
purlGTN:F00038 |
FAQs |
Importing data from a data library
|
|
|
|
purlGTN:F00039 |
FAQs |
Importing data from remote files
|
|
|
|
purlGTN:F00040 |
FAQs |
Importing via links
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|
|
|
purlGTN:F00129 |
FAQs |
Importación por medio de enlaces
|
|
|
|
purlGTN:F00178 |
FAQs |
Importer via un lien
|
|
|
|
purlGTN:F00041 |
FAQs |
Understanding job statuses
|
|
|
|
purlGTN:F00042 |
FAQs |
Moving datasets between Galaxy servers
|
|
|
|
purlGTN:F00043 |
FAQs |
Datasets not downloading at all
|
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|
|
purlGTN:F00044 |
FAQs |
Purging datasets
|
|
|
|
purlGTN:F00045 |
FAQs |
Quotas for datasets and histories
|
|
|
|
purlGTN:F00046 |
FAQs |
Renaming a dataset
|
|
|
|
purlGTN:F00047 |
FAQs |
Upload few files (1-10)
|
|
|
|
purlGTN:F00048 |
FAQs |
Upload many files (>10) via FTP
|
|
|
|
purlGTN:F00049 |
FAQs |
Working with deleted datasets
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|
|
|
purlGTN:F00050 |
FAQs |
Working with very large fasta datasets
|
|
|
|
purlGTN:F00051 |
FAQs |
Working with very large fastq datasets
|
|
|
|
purlGTN:F00052 |
FAQs |
Working with GFF GFT GTF2 GFF3 reference annotation
|
|
|
|
purlGTN:F00053 |
FAQs |
Using compressed fastq data as tool inputs
|
|
|
|
purlGTN:F00054 |
FAQs |
Best practices for loading fastq data into Galaxy
|
|
|
|
purlGTN:F00055 |
FAQs |
How do `fastq.gz` datasets relate to the `.fastqsanger` datatype metadata assignment?
|
|
|
|
purlGTN:F00056 |
FAQs |
Compressed FASTQ files, (`*.gz`)
|
|
|
|
purlGTN:F00057 |
FAQs |
How to format fastq data for tools that require .fastqsanger format?
|
|
|
|
purlGTN:F00058 |
FAQs |
FASTQ files: `fastq` vs `fastqsanger` vs ..
|
|
|
|
purlGTN:F00059 |
FAQs |
Identifying and formatting Tabular Datasets
|
|
|
|
purlGTN:F00060 |
FAQs |
Understanding Datatypes
|
|
|
|
purlGTN:F00061 |
FAQs |
How can I upload data using EBI-SRA?
|
|
|
|
purlGTN:F00062 |
FAQs |
Data retrieval with “NCBI SRA Tools” (fastq-dump)
|
|
|
|
purlGTN:F00063 |
FAQs |
NCBI SRA sourced fastq data
|
|
|
|
purlGTN:F00333 |
FAQs |
The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts?
|
Transcriptomics |
|
|
purlGTN:F00299 |
FAQs |
What software tools are available to determine taxonomic composition from mass spectrometry data?
|
Proteomics |
|
|
purlGTN:F00331 |
FAQs |
Could I use a different p-adj value for filtering differentially expressed genes?
|
Transcriptomics |
|
|
purlGTN:F00329 |
FAQs |
I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
|
Transcriptomics |
|
|
purlGTN:F00196 |
FAQs |
How to read a Diff
|
Galaxy Server administration |
|
|
purlGTN:F00226 |
FAQs |
Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
|
Single Cell |
|
|
purlGTN:F00278 |
FAQs |
What is the principle of an enrichment analysis?
|
Proteomics |
|
|
purlGTN:F00246 |
FAQs |
My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ?
|
Development in Galaxy |
|
|
purlGTN:F00247 |
FAQs |
`docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory`
|
Development in Galaxy |
|
|
purlGTN:F00260 |
FAQs |
Where can I find example queries for use in the cloud and elsewhere?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00148 |
FAQs |
How does the GTN ensure our training materials are FAIR?
|
|
|
|
purlGTN:F00224 |
FAQs |
FASTQ format
|
Sequence analysis |
|
|
purlGTN:F00267 |
FAQs |
Why do we use FASTQ interlacer and not the FASTQ joiner?
|
Metagenomics |
|
|
purlGTN:F00064 |
FAQs |
Using the Scratchbook to view multiple datasets
|
|
|
|
purlGTN:F00130 |
FAQs |
Uso del cuaderno de apuntes para ver varios conjuntos de datos
|
|
|
|
purlGTN:F00217 |
FAQs |
UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?
|
Introduction to Galaxy Analyses |
|
|
purlGTN:F00322 |
FAQs |
My Scanpy FindMarkers step is giving me an empty table
|
Single Cell |
|
|
purlGTN:F00215 |
FAQs |
Flatten a list of list of paired datasets into a list of paired datasets
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00248 |
FAQs |
What file/data formats are defined for I/O in Galaxy?
|
Development in Galaxy |
|
|
purlGTN:F00300 |
FAQs |
Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
|
Proteomics |
|
|
purlGTN:F00317 |
FAQs |
Where can I read more about Quality Control of data?
|
Sequence analysis |
|
|
purlGTN:F00197 |
FAQs |
Blank page or no CSS/JavaScript
|
Galaxy Server administration |
|
|
purlGTN:F00198 |
FAQs |
How many mules?
|
Galaxy Server administration |
|
|
purlGTN:F00199 |
FAQs |
Debugging tool errors
|
Galaxy Server administration |
|
|
purlGTN:F00200 |
FAQs |
Debugging tool memory errors
|
Galaxy Server administration |
|
|
purlGTN:F00201 |
FAQs |
Tool missing from Galaxy
|
Galaxy Server administration |
|
|
purlGTN:F00202 |
FAQs |
Galaxy UI is slow
|
Galaxy Server administration |
|
|
purlGTN:F00357 |
FAQs |
Updating from 22.01 to 23.0 with Ansible
|
Galaxy Server administration |
|
|
purlGTN:F00218 |
FAQs |
My Galaxy looks different than in the tutorial/video
|
Introduction to Galaxy Analyses |
|
|
purlGTN:F00149 |
FAQs |
Are there any upcoming events focused on Galaxy Training?
|
|
|
|
purlGTN:F00180 |
FAQs |
Compatible Versions of Galaxy
|
|
|
|
purlGTN:F00150 |
FAQs |
Ways to use Galaxy
|
|
|
|
purlGTN:F00151 |
FAQs |
What is Galaxy?
|
|
|
|
purlGTN:F00279 |
FAQs |
What is Gene Ontology (GO)?
|
Proteomics |
|
|
purlGTN:F00227 |
FAQs |
What exactly is a ‘Gene profile’?
|
Single Cell |
|
|
purlGTN:P00002 |
|
Genome annotation for eukaryotes genome annotationeukaryote |
|
|
|
purlGTN:P00003 |
|
Genome annotation for prokaryotes genome annotationprokaryote |
|
|
|
purlGTN:F00152 |
FAQs |
How can I load data?
|
|
|
|
purlGTN:F00244 |
FAQs |
Where can I get planemo?
|
Development in Galaxy |
|
|
purlGTN:F00203 |
FAQs |
Using Git With Ansible Vaults
|
Galaxy Server administration |
|
|
purlGTN:F00204 |
FAQs |
Time to git commit
|
Galaxy Server administration |
|
|
purlGTN:F00205 |
FAQs |
Galaxy Admin Training Path
|
Galaxy Server administration |
|
|
purlGTN:F00153 |
FAQs |
What is this website?
|
|
|
|
purlGTN:F00154 |
FAQs |
How can I advertise the training materials on my posters?
|
|
|
|
purlGTN:F00155 |
FAQs |
What audiences are the tutorials for?
|
|
|
|
purlGTN:F00156 |
FAQs |
How can I cite the GTN?
|
|
|
|
purlGTN:F00157 |
FAQs |
How is the content licensed?
|
|
|
|
purlGTN:F00352 |
FAQs |
What licenses are used in the GTN?
|
|
|
|
purlGTN:F00158 |
FAQs |
Creating a GTN News post
|
|
|
|
purlGTN:F00159 |
FAQs |
GTN Stats
|
|
|
|
purlGTN:F00160 |
FAQs |
Sustainability of the training-material and metadata
|
|
|
|
purlGTN:F00161 |
FAQs |
What are the tutorials for?
|
|
|
|
purlGTN:F00162 |
FAQs |
Adding workflow tests with Planemo
|
|
|
|
purlGTN:F00256 |
FAQs |
Changing the heatmap colours
|
Epigenetics |
|
|
purlGTN:F00065 |
FAQs |
Copy a dataset between histories
|
|
|
|
purlGTN:F00179 |
FAQs |
Créer un nouvel history
|
|
|
|
purlGTN:F00066 |
FAQs |
Creating a new history
|
|
|
|
purlGTN:F00131 |
FAQs |
Para la creación de un historial nuevo
|
|
|
|
purlGTN:F00067 |
FAQs |
Downloading histories
|
|
|
|
purlGTN:F00068 |
FAQs |
Find all Histories and purge (aka permanently delete)
|
|
|
|
purlGTN:F00069 |
FAQs |
Finding Histories
|
|
|
|
purlGTN:F00070 |
FAQs |
Importing a history
|
|
|
|
purlGTN:F00071 |
FAQs |
Renaming a history
|
|
|
|
purlGTN:F00132 |
FAQs |
Cambiando el nombre de un historial
|
|
|
|
purlGTN:F00072 |
FAQs |
Searching your history
|
|
|
|
purlGTN:F00073 |
FAQs |
Finding and working with "Histories shared with me"
|
|
|
|
purlGTN:F00074 |
FAQs |
Sharing your History
|
|
|
|
purlGTN:F00133 |
FAQs |
Compartiendo un historial
|
|
|
|
purlGTN:F00075 |
FAQs |
Transfer entire histories from one Galaxy server to another
|
|
|
|
purlGTN:F00076 |
FAQs |
Undeleting history
|
|
|
|
purlGTN:F00077 |
FAQs |
Unsharing unwanted histories
|
|
|
|
purlGTN:F00342 |
FAQs |
What does `^.*Gallus|Homo|Bos.*$` mean?
|
Metagenomics |
|
|
purlGTN:F00343 |
FAQs |
For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?
|
Metagenomics |
|
|
purlGTN:F00211 |
FAQs |
Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?
|
Assembly |
|
|
purlGTN:F00239 |
FAQs |
Which icons are available to use in my tutorial?
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00344 |
FAQs |
From where can I import other genomes?
|
Metagenomics |
|
|
purlGTN:F00334 |
FAQs |
When is the "infer experiment" tool used in practice?
|
Transcriptomics |
|
|
purlGTN:F00275 |
FAQs |
The input for a tool is not listed in the dropdown
|
Metagenomics |
|
|
purlGTN:F00272 |
FAQs |
The input for a tool is not listed in the dropdown
|
Metagenomics |
|
|
purlGTN:F00206 |
FAQs |
Install tools via the Admin UI
|
Galaxy Server administration |
|
|
purlGTN:F00164 |
FAQs |
What are the best practices for teaching with Galaxy?
|
|
|
|
purlGTN:F00165 |
FAQs |
What Galaxy instance should I use for my training?
|
|
|
|
purlGTN:F00166 |
FAQs |
How do I get help?
|
|
|
|
purlGTN:F00167 |
FAQs |
Where do I start?
|
|
|
|
purlGTN:F00079 |
FAQs |
Launch JupyterLab
|
|
|
|
purlGTN:F00080 |
FAQs |
Open a Terminal in Jupyter
|
|
|
|
purlGTN:F00081 |
FAQs |
Open interactive tool
|
|
|
|
purlGTN:F00082 |
FAQs |
Knitting RMarkdown documents in RStudio
|
|
|
|
purlGTN:F00083 |
FAQs |
Launch RStudio
|
|
|
|
purlGTN:F00084 |
FAQs |
Learning with RMarkdown in RStudio
|
|
|
|
purlGTN:F00085 |
FAQs |
Stop RStudio
|
|
|
|
purlGTN:P00004 |
|
Introduction to Galaxy and Ecological data analysis beginner |
|
|
|
purlGTN:P00005 |
|
Introduction to Galaxy and Sequence analysis beginner |
|
|
|
purlGTN:P00006 |
|
From R to Machine Learning; an introductory course beginner |
|
|
|
purlGTN:P00007 |
|
Introduction to Galaxy and Single Cell RNA Sequence analysis beginner |
|
|
|
purlGTN:P00012 |
|
Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding beginner |
|
|
|
purlGTN:P00013 |
|
Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling beginner |
|
|
|
purlGTN:P00014 |
|
Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration beginner |
|
|
|
purlGTN:P00015 |
|
Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery beginner |
|
|
|
purlGTN:P00016 |
|
Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme beginner |
|
|
|
purlGTN:F00168 |
FAQs |
What information should I include when reporting a problem?
|
|
|
|
purlGTN:F00315 |
FAQs |
JBrowse is taking a long time to complete?
|
Sequence analysis |
|
|
purlGTN:F00249 |
FAQs |
First job I submitted remains grey or running for a long time - is it broken?
|
Development in Galaxy |
|
|
purlGTN:F00345 |
FAQs |
Is there a way to filter on the Kalimari database?
|
Metagenomics |
|
|
purlGTN:F00338 |
FAQs |
TB Variant Report crashes (with an error about KeyError: 'protein')
|
Variant Analysis |
|
|
purlGTN:F00221 |
FAQs |
Kraken2 and the k-mer approach for taxonomy classification
|
Metagenomics |
|
|
purlGTN:F00169 |
FAQs |
How can I get help?
|
|
|
|
purlGTN:F00170 |
FAQs |
Where do I start?
|
|
|
|
purlGTN:F00171 |
FAQs |
Where can I run the hands-on tutorials?
|
|
|
|
purlGTN:F00172 |
FAQs |
How do I use this material?
|
|
|
|
purlGTN:F00213 |
FAQs |
Defining a Learning Pathway
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00207 |
FAQs |
Library Permission Issues
|
Galaxy Server administration |
|
|
purlGTN:F00250 |
FAQs |
Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed?
|
Development in Galaxy |
|
|
purlGTN:F00219 |
FAQs |
My jobs are not running / I cannot see the history overview menu
|
Introduction to Galaxy Analyses |
|
|
purlGTN:F00208 |
FAQs |
Failing all jobs from a specific user
|
Galaxy Server administration |
|
|
purlGTN:F00209 |
FAQs |
Mapping Jobs to Specific Storage By User
|
Galaxy Server administration |
|
|
purlGTN:F00287 |
FAQs |
When can you use (or cannot use) Match between runs in MaxQuant?
|
Proteomics |
|
|
purlGTN:F00288 |
FAQs |
Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.
|
Proteomics |
|
|
purlGTN:F00261 |
FAQs |
Where can I find the full listing and description of the columns in each metadata table?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:P00008 |
|
Metagenomics data processing and analysis for microbiome microbiome |
|
|
|
purlGTN:F00210 |
FAQs |
Got lost along the way?
|
Galaxy Server administration |
|
|
purlGTN:F00276 |
FAQs |
Where can I read more about this analysis?
|
Metagenomics |
|
|
purlGTN:F00273 |
FAQs |
Where can I read more about this analysis?
|
Metagenomics |
|
|
purlGTN:F00289 |
FAQs |
If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).
|
Proteomics |
|
|
purlGTN:F00268 |
FAQs |
Can we use the ASaiM-MT workflow on multiple input files at the same time?
|
Metagenomics |
|
|
purlGTN:F00318 |
FAQs |
MultiQC error for your FastQC reports?
|
Sequence analysis |
|
|
purlGTN:F00313 |
FAQs |
In the MVP platform, is it possible to view the genomic location of all the peptides?
|
Proteomics |
|
|
purlGTN:F00241 |
FAQs |
I cannot run client tests because yarn is not installed.
|
Development in Galaxy |
|
|
purlGTN:F00290 |
FAQs |
What does it mean to normalize the LFQ intensities?
|
Proteomics |
|
|
purlGTN:F00355 |
FAQs |
Notebook-based tutorials can give different outputs
|
Single Cell |
|
|
purlGTN:F00262 |
FAQs |
When will aligned read objects be available for other data types?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00291 |
FAQs |
Does MaxQuant give as output possibility the PSMs and PEPs?
|
Proteomics |
|
|
purlGTN:F00319 |
FAQs |
When I get a warning for base per sequence content, what should I do?
|
Sequence analysis |
|
|
purlGTN:F00237 |
FAQs |
Running more than one round of Pilon polishing
|
Assembly |
|
|
purlGTN:F00251 |
FAQs |
Only one Planemo test runs at a time. Why doesn't the server allow more than one at once?
|
Development in Galaxy |
|
|
purlGTN:F00323 |
FAQs |
On Scanpy PlotEmbed, the tool is failing
|
Single Cell |
|
|
purlGTN:F00324 |
FAQs |
On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
|
Single Cell |
|
|
purlGTN:F00238 |
FAQs |
Can we polish the assembly with long reads too?
|
Assembly |
|
|
purlGTN:F00086 |
FAQs |
Getting your API key
|
|
|
|
purlGTN:F00308 |
FAQs |
Example histories for the proteogenomics tutorials
|
Proteomics |
|
|
purlGTN:F00309 |
FAQs |
Can I use these workflows on datasets generated from our laboratory?
|
Proteomics |
|
|
purlGTN:F00310 |
FAQs |
The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
|
Proteomics |
|
|
purlGTN:F00311 |
FAQs |
What kind of variants are seen in the output?
|
Proteomics |
|
|
purlGTN:F00327 |
FAQs |
How do I know what protocol my data was sequenced with?
|
Single Cell |
|
|
purlGTN:F00351 |
FAQs |
Debugging Memory Leaks
|
Galaxy Server administration |
|
|
purlGTN:P00009 |
|
Introductory Python pythonreal-course |
|
|
|
purlGTN:F00263 |
FAQs |
Why don't the aligned read files have quality scores?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00350 |
FAQs |
Quality Scores
|
Sequence analysis |
|
|
purlGTN:F00332 |
FAQs |
Can I use alternative tools for the Quantification step?
|
Transcriptomics |
|
|
purlGTN:F00292 |
FAQs |
For the “quantitation method” what is the default if I just leave it as “None”? Label free?
|
Proteomics |
|
|
purlGTN:F00266 |
FAQs |
Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results?
|
Introduction to Galaxy Analyses |
|
|
purlGTN:F00328 |
FAQs |
Are Barcodes always on R1 and Sequence data on R2?
|
Single Cell |
|
|
purlGTN:F00087 |
FAQs |
How to use Custom Reference Genomes?
|
|
|
|
purlGTN:F00088 |
FAQs |
Sorting Reference Genome
|
|
|
|
purlGTN:F00089 |
FAQs |
Troubleshooting Custom Genome fasta
|
|
|
|
purlGTN:F00346 |
FAQs |
Isn't it awkward to find so many humans sequences there, since we filter for them before?
|
Metagenomics |
|
|
purlGTN:F00358 |
FAQs |
Preparing materials for asynchronous learning: CYOA
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00359 |
FAQs |
Preparing materials for asynchronous learning: FAQs
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00360 |
FAQs |
Preparing materials for asynchronous learning: Self-Study
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00361 |
FAQs |
Preparing materials for asynchronous learning: Tips
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00252 |
FAQs |
Is the ToolFactory a complete replacement for manual tool building?
|
Development in Galaxy |
|
|
purlGTN:F00223 |
FAQs |
Additional resources to learn more about proteomic data analysis
|
Proteomics |
|
|
purlGTN:F00301 |
FAQs |
Can I use these workflows on datasets generated from our laboratory?
|
Proteomics |
|
|
purlGTN:F00335 |
FAQs |
Is it possible to visualize the RNA STAR bam file using the JBrowse tool?
|
Transcriptomics |
|
|
purlGTN:F00336 |
FAQs |
RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'?
|
Transcriptomics |
|
|
purlGTN:F00339 |
FAQs |
My snippy is running for a very long time. Is this normal?
|
Variant Analysis |
|
|
purlGTN:F00265 |
FAQs |
What should I do special if on usegalaxy.be?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00302 |
FAQs |
Which search algorithms are recommended for searching the metaproteomics data?
|
Proteomics |
|
|
purlGTN:F00314 |
FAQs |
How many search engines can you use in SearchGUI?
|
Proteomics |
|
|
purlGTN:F00303 |
FAQs |
I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?
|
Proteomics |
|
|
purlGTN:F00242 |
FAQs |
When I try to run a Selenium test, I get an error
|
Development in Galaxy |
|
|
purlGTN:F00090 |
FAQs |
Illumina MiSeq sequencing
|
|
|
|
purlGTN:F00091 |
FAQs |
Nanopore sequencing
|
|
|
|
purlGTN:F00293 |
FAQs |
How many proteins can be identified and quantified in shotgun proteomics?
|
Proteomics |
|
|
purlGTN:F00353 |
FAQs |
Use our single cell Galaxy instance
|
Single Cell |
|
|
purlGTN:F00269 |
FAQs |
Can this ASaiM workflow be used for single-end data?
|
Metagenomics |
|
|
purlGTN:S00080 |
Slides |
Introduction to proteomics, protein identification, quantification and statistical modelling
|
Proteomics |
|
|
purlGTN:S00039 |
Slides |
The Pangeo ecosystem climate |
Climate |
|
15m |
purlGTN:S00036 |
Slides |
Functionally Assembled Terrestrial Ecosystem Simulator (FATES) climateecology |
Climate |
|
30m |
purlGTN:S00037 |
Slides |
Introduction to climate data
|
Climate |
|
|
purlGTN:S00038 |
Slides |
Pangeo ecosystem 101 for everyone climate |
Climate |
|
15m |
purlGTN:S00042 |
Slides |
Overview of the Galaxy Training Material
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:S00040 |
Slides |
Creating Slides
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:S00041 |
Slides |
Contributing with GitHub via command-line
|
Contributing to the Galaxy Training Material |
|
30m |
purlGTN:S00099 |
Slides |
Introduction to Variant analysis
|
Variant Analysis |
|
|
purlGTN:S00060 |
Slides |
Introduction to DNA Methylation data analysis
|
Epigenetics |
|
|
purlGTN:S00058 |
Slides |
ChIP-seq data analysis
|
Epigenetics |
|
15M |
purlGTN:S00057 |
Slides |
EWAS Epigenome-Wide Association Studies Introduction
|
Epigenetics |
|
|
purlGTN:S00059 |
Slides |
Introduction to ChIP-Seq data analysis
|
Epigenetics |
|
|
purlGTN:S00056 |
Slides |
Introduction to ATAC-Seq data analysis
|
Epigenetics |
|
30m |
purlGTN:S00071 |
Slides |
Nucleoli Segmentation & Feature Extraction using CellProfiler
|
Imaging |
|
4H |
purlGTN:S00078 |
Slides |
Introduction to metagenomics
|
Metagenomics |
|
|
purlGTN:S00079 |
Slides |
Introduction to metatranscriptomics
|
Metagenomics |
|
|
purlGTN:S00101 |
Slides |
Visualisations in Galaxy
|
Visualisation |
|
|
purlGTN:S00112 |
Slides |
Friends Don't Let Friends Make Bad Graphs
|
Visualisation |
|
|
purlGTN:S00100 |
Slides |
Circos
|
Visualisation |
|
|
purlGTN:S00102 |
Slides |
JBrowse
|
Visualisation |
|
|
purlGTN:S00109 |
Slides |
Bioinformatics Data Types and Databases
|
Foundations of Data Science |
|
1h |
purlGTN:S00047 |
Slides |
Tool Dependencies and Containers
|
Development in Galaxy |
|
45m |
purlGTN:S00053 |
Slides |
Visualizations: JavaScript Plugins
|
Development in Galaxy |
|
1h |
purlGTN:S00051 |
Slides |
Tool development and integration into Galaxy
|
Development in Galaxy |
|
6h |
purlGTN:S00046 |
Slides |
Prerequisites for building software/conda packages
|
Development in Galaxy |
|
1h |
purlGTN:S00049 |
Slides |
Galaxy Interactive Tours
|
Development in Galaxy |
|
3h |
purlGTN:S00052 |
Slides |
Tool Shed: sharing Galaxy tools
|
Development in Galaxy |
|
3h |
purlGTN:S00043 |
Slides |
Galaxy Code Architecture
|
Development in Galaxy |
|
150m |
purlGTN:S00048 |
Slides |
Galaxy Interactive Environments
|
Development in Galaxy |
|
90m |
purlGTN:S00045 |
Slides |
Tool Dependencies and Conda
|
Development in Galaxy |
|
75m |
purlGTN:S00050 |
Slides |
Introduction to the ToolFactory tutorial.
|
Development in Galaxy |
|
|
purlGTN:S00054 |
Slides |
Generic plugins
|
Development in Galaxy |
|
90m |
purlGTN:S00044 |
Slides |
Scripting Galaxy using the API and BioBlend
|
Development in Galaxy |
|
2h |
purlGTN:S00055 |
Slides |
Galaxy Webhooks
|
Development in Galaxy |
|
1h |
purlGTN:S00005 |
Slides |
Connecting Galaxy to a compute cluster features |
Galaxy Server administration |
|
|
purlGTN:S00024 |
Slides |
Terraform
|
Galaxy Server administration |
|
|
purlGTN:S00017 |
Slides |
Galaxy Monitoring with Telegraf and Grafana
|
Galaxy Server administration |
|
|
purlGTN:S00012 |
Slides |
Galaxy Monitoring
|
Galaxy Server administration |
|
|
purlGTN:S00002 |
Slides |
Galaxy Installation with Ansible
|
Galaxy Server administration |
|
|
purlGTN:S00008 |
Slides |
Galactic Database
|
Galaxy Server administration |
|
|
purlGTN:S00014 |
Slides |
Galaxy Interactive Tools
|
Galaxy Server administration |
|
|
purlGTN:S00020 |
Slides |
Running Jobs on Remote Resources with Pulsar jobs |
Galaxy Server administration |
|
60m |
purlGTN:S00103 |
Slides |
Server Maintenance: Cleanup, Backup, and Restoration
|
Galaxy Server administration |
|
30m |
purlGTN:S00004 |
Slides |
Galaxy on the Cloud
|
Galaxy Server administration |
|
|
purlGTN:S00025 |
Slides |
Galaxy Tool Management with Ephemeris
|
Galaxy Server administration |
|
|
purlGTN:S00015 |
Slides |
Galaxy from an administrator's point of view
|
Galaxy Server administration |
|
20m |
purlGTN:S00028 |
Slides |
uWSGI
|
Galaxy Server administration |
|
|
purlGTN:S00022 |
Slides |
Server: Other
|
Galaxy Server administration |
|
1h |
purlGTN:S00007 |
Slides |
Storage Management
|
Galaxy Server administration |
|
|
purlGTN:S00001 |
Slides |
Ansible
|
Galaxy Server administration |
|
|
purlGTN:S00026 |
Slides |
Galaxy Troubleshooting
|
Galaxy Server administration |
|
|
purlGTN:S00009 |
Slides |
Empathy
|
Galaxy Server administration |
|
|
purlGTN:S00003 |
Slides |
Galaxy and Celery
|
Galaxy Server administration |
|
|
purlGTN:S00027 |
Slides |
User, Role, Group, Quota, and Authentication managment
|
Galaxy Server administration |
|
15m |
purlGTN:S00013 |
Slides |
Galaxy Monitoring with gxadmin
|
Galaxy Server administration |
|
|
purlGTN:S00011 |
Slides |
Docker and Galaxy
|
Galaxy Server administration |
|
1h |
purlGTN:S00010 |
Slides |
External Authentication
|
Galaxy Server administration |
|
|
purlGTN:S00006 |
Slides |
Reference Data with CVMFS
|
Galaxy Server administration |
|
|
purlGTN:S00000 |
Slides |
Advanced customisation of a Galaxy instance
|
Galaxy Server administration |
|
|
purlGTN:S00019 |
Slides |
Gearing towards production
|
Galaxy Server administration |
|
|
purlGTN:S00018 |
Slides |
Storage Management
|
Galaxy Server administration |
|
|
purlGTN:S00023 |
Slides |
Controlling Galaxy with systemd or Supervisor
|
Galaxy Server administration |
|
|
purlGTN:S00021 |
Slides |
Reference Genomes in Galaxy
|
Galaxy Server administration |
|
|
purlGTN:S00082 |
Slides |
Quality Control
|
Sequence analysis |
|
1h |
purlGTN:S00081 |
Slides |
Mapping
|
Sequence analysis |
|
1h |
purlGTN:S00072 |
Slides |
A Short Introduction to Galaxy
|
Introduction to Galaxy Analyses |
|
|
purlGTN:S00073 |
Slides |
Introduction to Galaxy
|
Introduction to Galaxy Analyses |
|
|
purlGTN:S00075 |
Slides |
Options for using Galaxy
|
Introduction to Galaxy Analyses |
|
|
purlGTN:S00110 |
Slides |
Automated Cell Annotation
|
Single Cell |
|
|
purlGTN:S00085 |
Slides |
Plates, Batches, and Barcodes
|
Single Cell |
|
1h |
purlGTN:S00087 |
Slides |
Clustering 3K PBMCs with Scanpy
|
Single Cell |
|
1H |
purlGTN:S00084 |
Slides |
An introduction to scRNA-seq data analysis
|
Single Cell |
Intermediate |
30m |
purlGTN:S00111 |
Slides |
Trajectory analysis
|
Single Cell |
|
|
purlGTN:S00086 |
Slides |
Dealing with Cross-Contamination in Fixed Barcode Protocols
|
Single Cell |
|
1h |
purlGTN:S00092 |
Slides |
Overview of the Galaxy Training Material for Instructors
|
Teaching and Hosting Galaxy training |
|
10M |
purlGTN:S00093 |
Slides |
Workshop Kickoff
|
Teaching and Hosting Galaxy training |
|
30m |
purlGTN:S00035 |
Slides |
Unicycler Assembly prokaryote |
Assembly |
|
4h |
purlGTN:S00034 |
Slides |
An introduction to get started in genome assembly and annotation
|
Assembly |
Introductory |
1h |
purlGTN:S00031 |
Slides |
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads covid19 |
Assembly |
|
4h |
purlGTN:S00032 |
Slides |
De Bruijn Graph Assembly
|
Assembly |
|
2h |
purlGTN:S00033 |
Slides |
An Introduction to Genome Assembly
|
Assembly |
|
30m |
purlGTN:S00030 |
Slides |
Genome assembly quality control.
|
Assembly |
Introductory |
|
purlGTN:S00029 |
Slides |
Deeper look into Genome Assembly algorithms
|
Assembly |
Intermediate |
|
purlGTN:S00105 |
Slides |
BioImage Model Zoo: Advanced models in one-click bioimageioimage analysis |
Image analysis using Deep Learning |
|
5m |
purlGTN:S00107 |
Slides |
Contribute to the BioImage.IO models bioimageioimage analysis |
Image analysis using Deep Learning |
|
10m |
purlGTN:S00106 |
Slides |
Welcome to the BioImage Model Zoo bioimageioimage analysis |
Image analysis using Deep Learning |
|
5m |
purlGTN:S00096 |
Slides |
Network Analysis with Heinz
|
Transcriptomics |
|
|
purlGTN:S00098 |
Slides |
Visualization of RNA-Seq results with CummeRbund
|
Transcriptomics |
|
1h |
purlGTN:S00094 |
Slides |
Introduction to Transcriptomics
|
Transcriptomics |
|
|
purlGTN:S00108 |
Slides |
Identification of non-canonical ORFs and their potential biological function
|
Transcriptomics |
|
|
purlGTN:S00095 |
Slides |
Whole transcriptome analysis of Arabidopsis thaliana
|
Transcriptomics |
|
|
purlGTN:S00097 |
Slides |
Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies
|
Transcriptomics |
|
|
purlGTN:S00064 |
Slides |
Submitting SARS-CoV-2 sequences to ENA
|
Using Galaxy and Managing your Data |
|
1h |
purlGTN:S00062 |
Slides |
Getting data into Galaxy
|
Using Galaxy and Managing your Data |
|
|
purlGTN:S00061 |
Slides |
Galaxy workflows in Dockstore
|
Using Galaxy and Managing your Data |
|
|
purlGTN:S00063 |
Slides |
Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2 ncbicovid19 |
Using Galaxy and Managing your Data |
|
10m |
purlGTN:S00089 |
Slides |
Feedforward neural networks (FNN)
Deep Learning - Part 1
|
Statistics and machine learning |
|
|
purlGTN:S00090 |
Slides |
Recurrent neural networks (RNN)
Deep Learning - Part 2
|
Statistics and machine learning |
|
|
purlGTN:S00088 |
Slides |
Convolutional neural networks (CNN)
Deep Learning - Part 3
|
Statistics and machine learning |
|
|
purlGTN:S00091 |
Slides |
Image classification in Galaxy with fruit 360 dataset
|
Statistics and machine learning |
|
2H |
purlGTN:S00068 |
Slides |
High Performance Computing for Pairwise Genome Comparison
|
Genome Annotation |
|
2h |
purlGTN:S00066 |
Slides |
Refining Genome Annotations with Apollo prokaryote |
Genome Annotation |
|
5m |
purlGTN:S00069 |
Slides |
Introduction to Genome Annotation
|
Genome Annotation |
Intermediate |
|
purlGTN:S00067 |
Slides |
Introduction to CRISPR screen analysis
|
Genome Annotation |
|
5m |
purlGTN:S00070 |
Slides |
Essential genes detection with Transposon insertion sequencing bacteriatnseqessential genes |
Genome Annotation |
|
7H |
purlGTN:S00065 |
Slides |
Genome annotation with Prokka prokaryote |
Genome Annotation |
|
1h |
purlGTN:S00076 |
Slides |
Introduction to Metabolomics
|
Metabolomics |
|
|
purlGTN:S00077 |
Slides |
Mass spectrometry: LC-MS preprocessing - advanced
|
Metabolomics |
|
|
purlGTN:F00316 |
FAQs |
What is a SNP?
|
Sequence analysis |
|
|
purlGTN:P00010 |
|
Introductory SQL pythonreal-course |
|
|
|
purlGTN:F00294 |
FAQs |
MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?
|
Proteomics |
|
|
purlGTN:F00337 |
FAQs |
In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean?
|
Transcriptomics |
|
|
purlGTN:F00304 |
FAQs |
What other methods are available to study the functional state of the microbiome within Galaxy?
|
Proteomics |
|
|
purlGTN:F00257 |
FAQs |
Is it possible to subsample some samples if you have more reads?
|
Epigenetics |
|
|
purlGTN:F00092 |
FAQs |
Where do I get more support?
|
|
|
|
purlGTN:F00093 |
FAQs |
Contacting Galaxy Administrators
|
|
|
|
purlGTN:F00222 |
FAQs |
What is Taxonomy?
|
Metagenomics |
|
|
purlGTN:F00228 |
FAQs |
Can RNA-seq techniques be applied to scRNA-seq?
|
Single Cell |
|
|
purlGTN:F00264 |
FAQs |
Are these data free to use and download?
|
Using Galaxy and Managing your Data |
|
|
purlGTN:F00295 |
FAQs |
Does MaxQuant in Galaxy support TMT, iTRAQ, etc.?
|
Proteomics |
|
|
purlGTN:F00340 |
FAQs |
Do I have to run the tools in the order of the tutorial?
|
Variant Analysis |
|
|
purlGTN:F00094 |
FAQs |
Changing the tool version
|
|
|
|
purlGTN:F00095 |
FAQs |
Organizing the tool panel
|
|
|
|
purlGTN:F00096 |
FAQs |
Where is the tool help?
|
|
|
|
purlGTN:F00097 |
FAQs |
Viewing tool logs (`stdout` and `stderr`)
|
|
|
|
purlGTN:F00098 |
FAQs |
If a Tool is Missing
|
|
|
|
purlGTN:F00099 |
FAQs |
Re-running a tool
|
|
|
|
purlGTN:F00135 |
FAQs |
Para volver a ejecutar una herramienta
|
|
|
|
purlGTN:F00100 |
FAQs |
Selecting a dataset collection as input
|
|
|
|
purlGTN:F00101 |
FAQs |
Select multiple datasets
|
|
|
|
purlGTN:F00102 |
FAQs |
Multipile similar tools available
|
|
|
|
purlGTN:F00103 |
FAQs |
Sorting Tools
|
|
|
|
purlGTN:F00104 |
FAQs |
Tool doesn't recognize input datasets
|
|
|
|
purlGTN:F00305 |
FAQs |
Which version of SearchGUI and PeptideShaker shall I use for this tutorial?
|
Proteomics |
|
|
purlGTN:P00011 |
|
Train the Trainers trainingtrainers |
|
|
|
purlGTN:F00330 |
FAQs |
I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
|
Transcriptomics |
|
|
purlGTN:F00105 |
FAQs |
Understanding 'canceled by admin' or cluster failure error messages
|
|
|
|
purlGTN:F00106 |
FAQs |
Understanding 'exceeds memory allocation' error messages
|
|
|
|
purlGTN:F00107 |
FAQs |
Understanding input error messages
|
|
|
|
purlGTN:F00108 |
FAQs |
Understanding ValueError error messages
|
|
|
|
purlGTN:F00109 |
FAQs |
Understanding walltime error messages
|
|
|
|
purlGTN:T00368 |
Hands-on |
Making clinical datasets FAIR fairopendata stewardship |
FAIR Data, Workflows, and Research |
|
1H |
purlGTN:T00361 |
Hands-on |
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data fairdata managementbioimaging |
FAIR Data, Workflows, and Research |
|
15m |
purlGTN:T00369 |
Hands-on |
Sequence data submission to ENA FAIRENA |
FAIR Data, Workflows, and Research |
|
1H |
purlGTN:T00362 |
Hands-on |
FAIR Bioimage Metadata fairdata managementbioimaging |
FAIR Data, Workflows, and Research |
|
15m |
purlGTN:T00350 |
Hands-on |
FAIR Galaxy Training Material fairgtntraining |
FAIR Data, Workflows, and Research |
|
30M |
purlGTN:T00339 |
Hands-on |
Best practices for workflows in GitHub repositories ro-cratejupyter-notebook |
FAIR Data, Workflows, and Research |
|
30M |
purlGTN:T00343 |
Hands-on |
Workflow Run RO-Crate Introduction ro-crate |
FAIR Data, Workflows, and Research |
|
30M |
purlGTN:T00341 |
Hands-on |
RO-Crate in Python ro-cratejupyter-notebook |
FAIR Data, Workflows, and Research |
|
30M |
purlGTN:T00349 |
Hands-on |
FAIR data management solutions fairdmpdata stewardship |
FAIR Data, Workflows, and Research |
|
10M |
purlGTN:T00348 |
Hands-on |
RO-Crate - Introduction
|
FAIR Data, Workflows, and Research |
Introductory |
30M |
purlGTN:T00342 |
Hands-on |
Submitting workflows to LifeMonitor ro-crate |
FAIR Data, Workflows, and Research |
|
30M |
purlGTN:T00340 |
Hands-on |
Exporting Workflow Run RO-Crates from Galaxy ro-crateworkflows |
FAIR Data, Workflows, and Research |
|
30m |
purlGTN:T00351 |
Hands-on |
FAIR in a nutshell fairopendata stewardship |
FAIR Data, Workflows, and Research |
|
10M |
purlGTN:T00216 |
Hands-on |
Label-free versus Labelled - How to Choose Your Quantitation Method DDA |
Proteomics |
Introductory |
15m |
purlGTN:T00222 |
Hands-on |
metaQuantome 1: Data creation microgalaxy |
Proteomics |
Intermediate |
1h |
purlGTN:T00215 |
Hands-on |
EncyclopeDIA DIA |
Proteomics |
|
6H |
purlGTN:T00228 |
Hands-on |
Peptide and Protein ID using OpenMS tools DDAHeLa |
Proteomics |
Advanced |
45m |
purlGTN:T00229 |
Hands-on |
Peptide and Protein ID using SearchGUI and PeptideShaker DDAHeLa |
Proteomics |
Introductory |
45m |
purlGTN:T00220 |
Hands-on |
MaxQuant and MSstats for the analysis of TMT data DDATMT |
Proteomics |
|
3H |
purlGTN:T00224 |
Hands-on |
metaQuantome 3: Taxonomy microgalaxy |
Proteomics |
Intermediate |
1h |
purlGTN:T00214 |
Hands-on |
Protein FASTA Database Handling DDA |
Proteomics |
Introductory |
30m |
purlGTN:T00233 |
Hands-on |
Proteogenomics 3: Novel peptide analysis proteogenomics |
Proteomics |
Intermediate |
30m |
purlGTN:T00223 |
Hands-on |
metaQuantome 2: Function microgalaxy |
Proteomics |
Intermediate |
1h |
purlGTN:T00231 |
Hands-on |
Proteogenomics 1: Database Creation proteogenomics |
Proteomics |
Intermediate |
30m |
purlGTN:T00230 |
Hands-on |
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) DDASILAC |
Proteomics |
Advanced |
1h |
purlGTN:T00235 |
Hands-on |
Secretome Prediction humanwork-in-progress |
Proteomics |
Intermediate |
30m |
purlGTN:T00213 |
Hands-on |
Biomarker candidate identification DDAhuman |
Proteomics |
|
3H |
purlGTN:T00217 |
Hands-on |
Mass spectrometry imaging: Loading and exploring MSI data mouseimaging |
Proteomics |
Introductory |
45m |
purlGTN:T00212 |
Hands-on |
Library Generation for DIA Analysis DIA |
Proteomics |
Intermediate |
1H |
purlGTN:T00221 |
Hands-on |
Metaproteomics tutorial microgalaxy |
Proteomics |
|
2h |
purlGTN:T00211 |
Hands-on |
DIA Analysis using OpenSwathWorkflow DIA |
Proteomics |
Intermediate |
2H |
purlGTN:T00234 |
Hands-on |
Annotating a protein list identified by LC-MS/MS experiments DDAhuman |
Proteomics |
|
1H |
purlGTN:T00219 |
Hands-on |
MaxQuant and MSstats for the analysis of label-free data label-free |
Proteomics |
Intermediate |
2H |
purlGTN:T00227 |
Hands-on |
Peptide Library Data Analysis
|
Proteomics |
Intermediate |
20m |
purlGTN:T00210 |
Hands-on |
Statistical analysis of DIA data DIA |
Proteomics |
Intermediate |
1H |
purlGTN:T00225 |
Hands-on |
Machine Learning Modeling of Anticancer Peptides MLcancer |
Proteomics |
Intermediate |
30m |
purlGTN:T00232 |
Hands-on |
Proteogenomics 2: Database Search proteogenomics |
Proteomics |
Intermediate |
15m |
purlGTN:T00226 |
Hands-on |
Detection and quantitation of N-termini (degradomics) via N-TAILS
|
Proteomics |
Intermediate |
1h |
purlGTN:T00218 |
Hands-on |
Label-free data analysis using MaxQuant DDAlabel-free |
Proteomics |
Introductory |
1H |
purlGTN:T00045 |
Hands-on |
Pangeo Notebook in Galaxy - Introduction to Xarray pangeointeractive-toolsjupyter-notebook |
Climate |
|
1H |
purlGTN:T00043 |
Hands-on |
Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab interactive-tools |
Climate |
|
6H |
purlGTN:T00041 |
Hands-on |
Getting your hands-on climate data
|
Climate |
|
1H |
purlGTN:T00042 |
Hands-on |
Functionally Assembled Terrestrial Ecosystem Simulator (FATES) interactive-tools |
Climate |
|
4H |
purlGTN:T00046 |
Hands-on |
Visualize Climate data with Panoply netCDF viewer interactive-tools |
Climate |
|
1H |
purlGTN:T00044 |
Hands-on |
Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools pangeo |
Climate |
|
1H |
purlGTN:T00274 |
Hands-on |
Evaluating and ranking a set of pathways based on multiple metrics
|
Synthetic Biology |
|
20M |
purlGTN:T00275 |
Hands-on |
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
|
Synthetic Biology |
|
30M |
purlGTN:T00273 |
Hands-on |
Designing plasmids encoding predicted pathways by using the BASIC assembly method
|
Synthetic Biology |
|
15M |
purlGTN:T00063 |
Hands-on |
Generating PDF artefacts of the website
|
Contributing to the Galaxy Training Material |
|
10m |
purlGTN:T00056 |
Hands-on |
Including a new topic
|
Contributing to the Galaxy Training Material |
|
30m |
purlGTN:T00066 |
Hands-on |
Running the GTN website online using GitPod
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00363 |
Hands-on |
FAIR Galaxy Training Material fairgtntraining |
Contributing to the Galaxy Training Material |
|
30M |
purlGTN:T00062 |
Hands-on |
Design and plan session, course, materials
|
Contributing to the Galaxy Training Material |
|
60m |
purlGTN:T00058 |
Hands-on |
Creating content in Markdown
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00068 |
Hands-on |
Teaching Python
|
Contributing to the Galaxy Training Material |
|
2h |
purlGTN:T00059 |
Hands-on |
Adding Quizzes to your Tutorial
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00071 |
Hands-on |
Adding auto-generated video to your slides
|
Contributing to the Galaxy Training Material |
|
20m |
purlGTN:T00067 |
Hands-on |
Principles of learning and how they apply to training and teaching
|
Contributing to the Galaxy Training Material |
|
2h |
purlGTN:T00070 |
Hands-on |
GTN Metadata
|
Contributing to the Galaxy Training Material |
|
10m |
purlGTN:T00065 |
Hands-on |
Contributing with GitHub via its interface
|
Contributing to the Galaxy Training Material |
|
20m |
purlGTN:T00055 |
Hands-on |
Updating diffs in admin training
|
Contributing to the Galaxy Training Material |
|
5m |
purlGTN:T00069 |
Hands-on |
Running the GTN website locally
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00057 |
Hands-on |
Creating a new tutorial
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00060 |
Hands-on |
Tools, Data, and Workflows for tutorials
|
Contributing to the Galaxy Training Material |
|
30m |
purlGTN:T00061 |
Hands-on |
Creating Interactive Galaxy Tours
|
Contributing to the Galaxy Training Material |
|
15m |
purlGTN:T00064 |
Hands-on |
Contributing with GitHub via command-line
|
Contributing to the Galaxy Training Material |
|
30m |
purlGTN:T00131 |
Hands-on |
Visualize EBV cube data with Panoply netCDF viewer interactive-toolsEBV cubeData visualization |
Ecology |
|
1H |
purlGTN:T00126 |
Hands-on |
Biodiversity data exploration taxonomic datadata quality |
Ecology |
|
1H |
purlGTN:T00132 |
Hands-on |
Preparing genomic data for phylogeny reconstruction phylogenydata handlingfunctional annotation |
Ecology |
|
3H |
purlGTN:T00333 |
Hands-on |
Sentinel 2 biodiversity Remote sensing |
Ecology |
|
48H |
purlGTN:T00125 |
Hands-on |
Compute and analyze biodiversity metrics with PAMPA toolsuite Species population EBV classCommunity composition EBV classEBV datasetEBV workflowmodeling |
Ecology |
|
2H |
purlGTN:T00130 |
Hands-on |
RAD-Seq to construct genetic maps RAD-seqGenetic composition EBV classEBV datasetEBV workflow |
Ecology |
|
8h |
purlGTN:T00134 |
Hands-on |
Regional GAM Species populations EBV classSpecies traits EBV classEBV datasetEBV workflow |
Ecology |
|
2h30m |
purlGTN:T00367 |
Hands-on |
QGIS Web Feature Services GISGeographical Information SystemWFSSpatial dataQGISMapsOGC |
Ecology |
|
0H30M |
purlGTN:T00124 |
Hands-on |
Metabarcoding/eDNA through Obitools Genetic composition EBV classCommunity composition EBV classEBV datasetEBV workfloweDNAMetabarcoding |
Ecology |
|
1H |
purlGTN:T00127 |
Hands-on |
Champs blocs indicators
|
Ecology |
|
1H |
purlGTN:T00128 |
Hands-on |
RAD-Seq de-novo data analysis RAD-seqGenetic composition EBV classSpecies populations EBV classEBV datasetEBV workflow |
Ecology |
|
8h |
purlGTN:T00129 |
Hands-on |
Cleaning GBIF data for the use in Ecology gbifdata managementdata cleaning |
Ecology |
|
0H30M |
purlGTN:T00332 |
Hands-on |
Obis marine indicators
|
Ecology |
|
1H |
purlGTN:T00135 |
Hands-on |
Species distribution modeling interactive-toolsmodelinggbifspecies populations EBV class |
Ecology |
|
1h |
purlGTN:T00133 |
Hands-on |
RAD-Seq Reference-based data analysis RAD-seqGenetic composition EBV classSpecies population EBV classEBV datasetEBV workflow |
Ecology |
|
8h |
purlGTN:T00136 |
Hands-on |
Visualization of Climate Data using NetCDF xarray Map Plotting pangeo |
Ecology |
Introductory |
1H |
purlGTN:T00314 |
Hands-on |
Calling variants in non-diploid systems prokaryotemicrogalaxy |
Variant Analysis |
|
1h30m |
purlGTN:T00320 |
Hands-on |
Trio Analysis using Synthetic Datasets from RD-Connect GPAP cyoa |
Variant Analysis |
|
2H |
purlGTN:T00317 |
Hands-on |
Somatic Variant Discovery from WES Data Using Control-FREEC
|
Variant Analysis |
|
3H |
purlGTN:T00319 |
Hands-on |
M. tuberculosis Variant Analysis prokaryoteone-healthmicrogalaxy |
Variant Analysis |
Intermediate |
2h |
purlGTN:T00318 |
Hands-on |
Identification of somatic and germline variants from tumor and normal sample pairs
|
Variant Analysis |
|
7h |
purlGTN:T00347 |
Hands-on |
Pox virus genome analysis from tiled-amplicon sequencing data virologyone-health |
Variant Analysis |
Advanced |
4H |
purlGTN:T00309 |
Hands-on |
Calling variants in diploid systems
|
Variant Analysis |
|
3h |
purlGTN:T00310 |
Hands-on |
Calling very rare variants
|
Variant Analysis |
|
3h |
purlGTN:T00312 |
Hands-on |
Mapping and molecular identification of phenotype-causing mutations
|
Variant Analysis |
|
2h |
purlGTN:T00313 |
Hands-on |
Microbial Variant Calling prokaryotemicrogalaxy |
Variant Analysis |
|
45m |
purlGTN:T00315 |
Hands-on |
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis covid19virologyone-health |
Variant Analysis |
|
1H |
purlGTN:T00308 |
Hands-on |
Avian influenza viral strain analysis from gene segment sequencing data virologyone-health |
Variant Analysis |
Intermediate |
4H |
purlGTN:T00316 |
Hands-on |
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data covid19virologyone-health |
Variant Analysis |
Intermediate |
3H |
purlGTN:T00311 |
Hands-on |
Exome sequencing data analysis for diagnosing a genetic disease
|
Variant Analysis |
|
5h |
purlGTN:T00138 |
Hands-on |
Identification of the binding sites of the Estrogen receptor ChIP-seqwork-in-progress |
Epigenetics |
|
3h |
purlGTN:T00140 |
Hands-on |
Formation of the Super-Structures on the Inactive X ChIP-seq |
Epigenetics |
|
3h |
purlGTN:T00143 |
Hands-on |
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) ChIP-seq |
Epigenetics |
|
3h |
purlGTN:T00139 |
Hands-on |
Infinium Human Methylation BeadChip
|
Epigenetics |
|
1h |
purlGTN:T00142 |
Hands-on |
DNA Methylation data analysis
|
Epigenetics |
|
3h |
purlGTN:T00137 |
Hands-on |
ATAC-Seq data analysis
|
Epigenetics |
|
3h |
purlGTN:T00141 |
Hands-on |
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
|
Epigenetics |
|
1h |
purlGTN:T00364 |
Hands-on |
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data fairdata managementbioimaging |
Imaging |
|
15m |
purlGTN:T00365 |
Hands-on |
FAIR Bioimage Metadata fairdata managementbioimaging |
Imaging |
|
15m |
purlGTN:T00334 |
Hands-on |
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
|
Imaging |
|
3H |
purlGTN:T00180 |
Hands-on |
Analyse HeLa fluorescence siRNA screen HeLa |
Imaging |
Intermediate |
1H |
purlGTN:T00182 |
Hands-on |
Object tracking using CellProfiler
|
Imaging |
|
1H |
purlGTN:T00183 |
Hands-on |
Nucleoli segmentation and feature extraction using CellProfiler
|
Imaging |
|
4H |
purlGTN:T00181 |
Hands-on |
Introduction to image analysis using Galaxy HeLa |
Imaging |
Introductory |
1H |
purlGTN:T00206 |
Hands-on |
16S Microbial Analysis with mothur (short) microgalaxy |
Metagenomics |
|
2h |
purlGTN:T00338 |
Hands-on |
Taxonomic Profiling and Visualization of Metagenomic Data metagenomicstaxonomic profilingmicrogalaxy |
Metagenomics |
Introductory |
2H |
purlGTN:T00201 |
Hands-on |
Analyses of metagenomics data - The global picture microgalaxy |
Metagenomics |
|
2H30M |
purlGTN:T00202 |
Hands-on |
Assembly of metagenomic sequencing data assemblymetagenomicsmicrogalaxy |
Metagenomics |
Introductory |
2H |
purlGTN:T00203 |
Hands-on |
Metatranscriptomics analysis using microbiome RNA-seq data metatranscriptomicsmicrogalaxy |
Metagenomics |
Introductory |
5H |
purlGTN:T00208 |
Hands-on |
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition microgalaxyNanopore data analysisPathogens detectionPhylogenetic treeHeatmapcyoa |
Metagenomics |
Introductory |
4h |
purlGTN:T00205 |
Hands-on |
16S Microbial Analysis with mothur (extended) microgalaxy |
Metagenomics |
|
6h |
purlGTN:T00200 |
Hands-on |
Identification of the micro-organisms in a beer using Nanopore sequencing nanoporebeercitizen sciencemetagenomicsmicrogalaxy |
Metagenomics |
Introductory |
1H |
purlGTN:T00204 |
Hands-on |
Metatranscriptomics analysis using microbiome RNA-seq data (short) metatranscriptomicsmicrogalaxy |
Metagenomics |
Introductory |
3H |
purlGTN:T00209 |
Hands-on |
Antibiotic resistance detection nanoporeplasmidsassemblyamrmicrogalaxy |
Metagenomics |
|
3h |
purlGTN:T00207 |
Hands-on |
16S Microbial analysis with Nanopore data nanoporemicrogalaxy |
Metagenomics |
|
2H |
purlGTN:T00373 |
Hands-on |
Ploting a Microbial Genome with Circos
|
Visualisation |
|
30m |
purlGTN:T00321 |
Hands-on |
Visualisation with Circos
|
Visualisation |
|
2h |
purlGTN:T00322 |
Hands-on |
Genomic Data Visualisation with JBrowse
|
Visualisation |
|
1h |
purlGTN:T00087 |
Hands-on |
Python - Files & CSV jupyter-notebook |
Foundations of Data Science |
Introductory |
1H30M |
purlGTN:T00072 |
Hands-on |
Version Control with Git
|
Foundations of Data Science |
|
65M |
purlGTN:T00081 |
Hands-on |
Advanced Python jupyter-notebook |
Foundations of Data Science |
Intermediate |
3H |
purlGTN:T00082 |
Hands-on |
Python - Argparse
|
Foundations of Data Science |
Intermediate |
30M |
purlGTN:T00098 |
Hands-on |
Python - Testing jupyter-notebook |
Foundations of Data Science |
Intermediate |
45M |
purlGTN:T00110 |
Hands-on |
SQL with R SQLRrmarkdown-notebookjupyter-notebook |
Foundations of Data Science |
Intermediate |
45M |
purlGTN:T00106 |
Hands-on |
Advanced SQL SQLjupyter-notebook |
Foundations of Data Science |
Introductory |
3H |
purlGTN:T00092 |
Hands-on |
Python - Coding Style jupyter-notebook |
Foundations of Data Science |
Intermediate |
30M |
purlGTN:T00076 |
Hands-on |
CLI basics bashjupyter-notebook |
Foundations of Data Science |
Introductory |
1H |
purlGTN:T00352 |
Hands-on |
Data Manipulation Olympics - JQ cyoajson |
Foundations of Data Science |
Introductory |
1h |
purlGTN:T00075 |
Hands-on |
CLI Educational Game - Bashcrawl gamebashjupyter-notebook |
Foundations of Data Science |
Intermediate |
2H |
purlGTN:T00102 |
Hands-on |
Advanced R in Galaxy R |
Foundations of Data Science |
Intermediate |
2H |
purlGTN:T00089 |
Hands-on |
Python - Functions jupyter-notebook |
Foundations of Data Science |
Introductory |
30M |
purlGTN:T00091 |
Hands-on |
Python - Lists & Strings & Dictionaries jupyter-notebook |
Foundations of Data Science |
Introductory |
1H |
purlGTN:T00078 |
Hands-on |
Data Manipulation Olympics - SQL cyoasqljupyter-notebook |
Foundations of Data Science |
Introductory |
1h |
purlGTN:T00107 |
Hands-on |
Introduction to SQL SQLjupyter-notebook |
Foundations of Data Science |
Introductory |
3H |
purlGTN:T00088 |
Hands-on |
Python - Flow Control jupyter-notebook |
Foundations of Data Science |
Introductory |
40M |
purlGTN:T00105 |
Hands-on |
Make & Snakemake
|
Foundations of Data Science |
Intermediate |
3H |
purlGTN:T00073 |
Hands-on |
Variant Calling Workflow
|
Foundations of Data Science |
|
50M |
purlGTN:T00096 |
Hands-on |
Plotting in Python jupyter-notebook |
Foundations of Data Science |
Intermediate |
1H |
purlGTN:T00360 |
Hands-on |
One protein along the UniProt page
|
Foundations of Data Science |
Introductory |
1H |
purlGTN:T00079 |
Hands-on |
Basics of using Git from the Command Line
|
Foundations of Data Science |
|
30m |
purlGTN:T00090 |
Hands-on |
Python - Globbing jupyter-notebook |
Foundations of Data Science |
Intermediate |
15M |
purlGTN:T00109 |
Hands-on |
SQL with Python SQLPythonjupyter-notebook |
Foundations of Data Science |
Intermediate |
45M |
purlGTN:T00353 |
Hands-on |
Data visualisation Olympics - Visualization in R cyoaRrmarkdown-notebookjupyter-notebook |
Foundations of Data Science |
Introductory |
1h |
purlGTN:T00093 |
Hands-on |
Python - Loops jupyter-notebook |
Foundations of Data Science |
Introductory |
40M |
purlGTN:T00085 |
Hands-on |
Conda Environments For Software Development condajupyter-notebook |
Foundations of Data Science |
Intermediate |
30M |
purlGTN:T00083 |
Hands-on |
Introduction to Python jupyter-notebook |
Foundations of Data Science |
Introductory |
5H |
purlGTN:T00074 |
Hands-on |
Advanced CLI in Galaxy bashjupyter-notebook |
Foundations of Data Science |
Intermediate |
2H |
purlGTN:T00094 |
Hands-on |
Python - Math jupyter-notebook |
Foundations of Data Science |
Introductory |
30M |
purlGTN:T00086 |
Hands-on |
Python - Try & Except jupyter-notebook |
Foundations of Data Science |
Introductory |
20M |
purlGTN:T00101 |
Hands-on |
Virtual Environments For Software Development jupyter-notebook |
Foundations of Data Science |
Intermediate |
30M |
purlGTN:T00099 |
Hands-on |
Python - Basic Types & Type Conversion jupyter-notebook |
Foundations of Data Science |
Introductory |
30M |
purlGTN:T00100 |
Hands-on |
Python - Type annotations jupyter-notebook |
Foundations of Data Science |
Intermediate |
30M |
purlGTN:T00095 |
Hands-on |
Python - Multiprocessing jupyter-notebook |
Foundations of Data Science |
Advanced |
30M |
purlGTN:T00359 |
Hands-on |
Learning about one gene across biological resources and formats
|
Foundations of Data Science |
Introductory |
1H |
purlGTN:T00104 |
Hands-on |
dplyr & tidyverse for data processing Rrmarkdown-notebookjupyter-notebook |
Foundations of Data Science |
Advanced |
1H |
purlGTN:T00097 |
Hands-on |
Python - Subprocess jupyter-notebook |
Foundations of Data Science |
Intermediate |
45M |
purlGTN:T00084 |
Hands-on |
Python - Introductory Graduation jupyter-notebook |
Foundations of Data Science |
Introductory |
1H30M |
purlGTN:T00103 |
Hands-on |
R basics in Galaxy interactive-toolsR |
Foundations of Data Science |
Introductory |
3H |
purlGTN:T00108 |
Hands-on |
SQL Educational Game - Murder Mystery gameSQLjupyter-notebook |
Foundations of Data Science |
Intermediate |
2H |
purlGTN:T00054 |
Hands-on |
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
|
Computational chemistry |
Intermediate |
2H |
purlGTN:T00053 |
Hands-on |
Setting up molecular systems
|
Computational chemistry |
Intermediate |
2H |
purlGTN:T00049 |
Hands-on |
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring covid19one-health |
Computational chemistry |
Intermediate |
2H |
purlGTN:T00050 |
Hands-on |
High Throughput Molecular Dynamics and Analysis
|
Computational chemistry |
Advanced |
3H |
purlGTN:T00048 |
Hands-on |
Protein-ligand docking
|
Computational chemistry |
Intermediate |
3H |
purlGTN:T00052 |
Hands-on |
Running molecular dynamics simulations using NAMD
|
Computational chemistry |
Intermediate |
3H |
purlGTN:T00047 |
Hands-on |
Analysis of molecular dynamics simulations
|
Computational chemistry |
Intermediate |
1H |
purlGTN:T00051 |
Hands-on |
Running molecular dynamics simulations using GROMACS
|
Computational chemistry |
Intermediate |
2H |
purlGTN:T00114 |
Hands-on |
Data source integration
|
Development in Galaxy |
|
10M |
purlGTN:T00117 |
Hands-on |
Creating Galaxy tools from Conda Through Deployment
|
Development in Galaxy |
|
3H |
purlGTN:T00112 |
Hands-on |
Contributing to BioBlend as a developer
|
Development in Galaxy |
|
3h |
purlGTN:T00116 |
Hands-on |
Galaxy Interactive Tools
|
Development in Galaxy |
|
3h |
purlGTN:T00120 |
Hands-on |
JavaScript plugins
|
Development in Galaxy |
|
1h |
purlGTN:T00115 |
Hands-on |
Debugging Galaxy
|
Development in Galaxy |
|
4h |
purlGTN:T00119 |
Hands-on |
ToolFactory: Generating Tools From More Complex Scripts
|
Development in Galaxy |
|
1H |
purlGTN:T00123 |
Hands-on |
Writing Automated Tests for Galaxy
|
Development in Galaxy |
|
3h |
purlGTN:T00118 |
Hands-on |
ToolFactory: Generating Tools From Simple Scripts
|
Development in Galaxy |
|
1H |
purlGTN:T00121 |
Hands-on |
Generic plugins
|
Development in Galaxy |
|
90m |
purlGTN:T00111 |
Hands-on |
Scripting Galaxy using the API and BioBlend jupyter-notebook |
Development in Galaxy |
Introductory |
2h |
purlGTN:T00113 |
Hands-on |
Contributing a New Feature to Galaxy Core
|
Development in Galaxy |
|
3H |
purlGTN:T00122 |
Hands-on |
Galaxy Webhooks
|
Development in Galaxy |
|
1h |
purlGTN:T00002 |
Hands-on |
Connecting Galaxy to a compute cluster jobsansiblegit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00025 |
Hands-on |
Upgrading Galaxy ansible |
Galaxy Server administration |
|
1h |
purlGTN:T00021 |
Hands-on |
Deploying a compute cluster in OpenStack via Terraform terraformdeployingcloud |
Galaxy Server administration |
|
60m |
purlGTN:T00015 |
Hands-on |
Galaxy Monitoring with Telegraf and Grafana ansiblemonitoringgit-gat |
Galaxy Server administration |
|
2h |
purlGTN:T00001 |
Hands-on |
Galaxy Installation with Ansible ansibledeployinggit-gat |
Galaxy Server administration |
|
2h30m |
purlGTN:T00010 |
Hands-on |
Galaxy Interactive Tools ansibleinteractive-tools |
Galaxy Server administration |
|
2h |
purlGTN:T00017 |
Hands-on |
Running Jobs on Remote Resources with Pulsar ansiblejobsgit-gat |
Galaxy Server administration |
|
60m |
purlGTN:T00324 |
Hands-on |
Server Maintenance: Cleanup, Backup, and Restoration ansibledeployinggit-gat |
Galaxy Server administration |
|
30m |
purlGTN:T00020 |
Hands-on |
How I learned to stop worrying and love the systemd ansiblesystemd |
Galaxy Server administration |
|
30m |
purlGTN:T00011 |
Hands-on |
Automation with Jenkins ansibleautomation |
Galaxy Server administration |
|
1h |
purlGTN:T00328 |
Hands-on |
Customizing the look of Galaxy (Manual)
|
Galaxy Server administration |
|
45m |
purlGTN:T00013 |
Hands-on |
Galaxy Installation on Kubernetes kubernetes |
Galaxy Server administration |
Intermediate |
30m |
purlGTN:T00325 |
Hands-on |
Deploying a Beacon v1 in Galaxy ga4ghbeacongit-gat |
Galaxy Server administration |
|
30m |
purlGTN:T00330 |
Hands-on |
Monitoring Galaxy and Pulsar with Sentry ansiblegit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00008 |
Hands-on |
Enable upload via FTP datagit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00024 |
Hands-on |
Performant Uploads with TUS
|
Galaxy Server administration |
|
30M |
purlGTN:T00023 |
Hands-on |
Galaxy Tool Management with Ephemeris toolsgit-gat |
Galaxy Server administration |
|
45m |
purlGTN:T00022 |
Hands-on |
Training Infrastructure as a Service (TIaaS) ansibletrainingjobsgit-gat |
Galaxy Server administration |
|
30m |
purlGTN:T00006 |
Hands-on |
Galaxy Database schema
|
Galaxy Server administration |
|
2h |
purlGTN:T00018 |
Hands-on |
Galaxy Monitoring with Reports ansiblemonitoringgit-gatbroken |
Galaxy Server administration |
|
30m |
purlGTN:T00005 |
Hands-on |
Data Libraries ansiblestoragegit-gat |
Galaxy Server administration |
|
30m |
purlGTN:T00327 |
Hands-on |
Customizing the look of Galaxy git-gat |
Galaxy Server administration |
|
45m |
purlGTN:T00000 |
Hands-on |
Ansible ansible |
Galaxy Server administration |
|
60m |
purlGTN:T00326 |
Hands-on |
Setting up Celery Workers for Galaxy ansiblegit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00009 |
Hands-on |
Galaxy Monitoring with gxadmin monitoringansiblegit-gat |
Galaxy Server administration |
|
30m |
purlGTN:T00007 |
Hands-on |
External Authentication authentication |
Galaxy Server administration |
|
30m |
purlGTN:T00004 |
Hands-on |
Reference Data with CVMFS without Ansible
|
Galaxy Server administration |
|
1h |
purlGTN:T00003 |
Hands-on |
Reference Data with CVMFS ansiblegit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00012 |
Hands-on |
Mapping Jobs to Destinations using TPV jobsgit-gat |
Galaxy Server administration |
|
2h |
purlGTN:T00323 |
Hands-on |
Use Apptainer containers for running Galaxy jobs jobsansiblegit-gat |
Galaxy Server administration |
|
1h |
purlGTN:T00026 |
Hands-on |
Deploying Wireguard for private mesh networking wireguardnetworking |
Galaxy Server administration |
|
60m |
purlGTN:T00027 |
Hands-on |
Deploying Tailscale/Headscale for private mesh networking wireguardnetworking |
Galaxy Server administration |
|
60m |
purlGTN:T00016 |
Hands-on |
Distributed Object Storage ansiblestorage |
Galaxy Server administration |
|
30m |
purlGTN:T00014 |
Hands-on |
Managing Galaxy on Kubernetes kubernetes |
Galaxy Server administration |
Intermediate |
30m |
purlGTN:T00329 |
Hands-on |
Reference Data with Data Managers
|
Galaxy Server administration |
|
1h |
purlGTN:T00356 |
Hands-on |
SARS-CoV-2 Viral Sample Alignment and Variant Visualization covid19 |
Sequence analysis |
Introductory |
1H |
purlGTN:T00236 |
Hands-on |
Removal of human reads from SARS-CoV-2 sequencing data covid19 |
Sequence analysis |
Intermediate |
1h |
purlGTN:T00238 |
Hands-on |
NCBI BLAST+ against the MAdLand
|
Sequence analysis |
|
15m |
purlGTN:T00239 |
Hands-on |
Quality Control
|
Sequence analysis |
Introductory |
1H30M |
purlGTN:T00237 |
Hands-on |
Mapping
|
Sequence analysis |
|
1h |
purlGTN:T00193 |
Hands-on |
IGV Introduction
|
Introduction to Galaxy Analyses |
|
2H |
purlGTN:T00190 |
Hands-on |
A short introduction to Galaxy español |
Introduction to Galaxy Analyses |
Introductory |
40m |
purlGTN:T00189 |
Hands-on |
From peaks to genes
|
Introduction to Galaxy Analyses |
Introductory |
3H |
purlGTN:T00188 |
Hands-on |
NGS data logistics
|
Introduction to Galaxy Analyses |
|
1H30M |
purlGTN:T00191 |
Hands-on |
Introduction to Genomics and Galaxy
|
Introduction to Galaxy Analyses |
Introductory |
2H30M |
purlGTN:T00184 |
Hands-on |
Data Manipulation Olympics cyoa |
Introduction to Galaxy Analyses |
Introductory |
1h |
purlGTN:T00187 |
Hands-on |
Galaxy 101 for everyone
|
Introduction to Galaxy Analyses |
Introductory |
1H30M |
purlGTN:T00192 |
Hands-on |
How to reproduce published Galaxy analyses
|
Introduction to Galaxy Analyses |
Introductory |
1H |
purlGTN:T00185 |
Hands-on |
Upload data to Galaxy
|
Introduction to Galaxy Analyses |
Introductory |
40m |
purlGTN:T00186 |
Hands-on |
Galaxy 101
|
Introduction to Galaxy Analyses |
Introductory |
1H |
purlGTN:T00144 |
Hands-on |
Tree thinking for tuberculosis evolution and epidemiology prokaryoteone-healthphylogeneticsmicrogalaxy |
Evolution |
Introductory |
1H |
purlGTN:T00145 |
Hands-on |
Identifying tuberculosis transmission links: from SNPs to transmission clusters prokaryoteone-healthmicrogalaxy |
Evolution |
Intermediate |
2H |
purlGTN:T00250 |
Hands-on |
Analysis of plant scRNA-Seq Data with Scanpy plantspaper-replication |
Single Cell |
|
2H |
purlGTN:T00255 |
Hands-on |
Single-cell quality control with scater
|
Single Cell |
|
1H |
purlGTN:T00253 |
Hands-on |
Downstream Single-cell RNA analysis with RaceID
|
Single Cell |
|
3H |
purlGTN:T00243 |
Hands-on |
Comparing inferred cell compositions using MuSiC deconvolution transcriptomics |
Single Cell |
|
1H |
purlGTN:T00256 |
Hands-on |
Understanding Barcodes
|
Single Cell |
|
2h |
purlGTN:T00249 |
Hands-on |
Inferring single cell trajectories (Monocle3) 10xpaper-replicationR |
Single Cell |
|
2H |
purlGTN:T00242 |
Hands-on |
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution transcriptomicsdata management |
Single Cell |
|
1H |
purlGTN:T00254 |
Hands-on |
Clustering 3K PBMCs with Scanpy 10x |
Single Cell |
|
5H |
purlGTN:T00252 |
Hands-on |
Pre-processing of 10X Single-Cell RNA Datasets 10x |
Single Cell |
|
1h |
purlGTN:T00246 |
Hands-on |
Combining single cell datasets after pre-processing 10xpaper-replication |
Single Cell |
|
1H |
purlGTN:T00244 |
Hands-on |
Inferring single cell trajectories (Scanpy, Python) 10xpaper-replicationPythonjupyter-notebook |
Single Cell |
|
2H |
purlGTN:T00335 |
Hands-on |
Pre-processing of 10X Single-Cell ATAC-seq Datasets 10xepigenetics |
Single Cell |
|
1h |
purlGTN:T00248 |
Hands-on |
Removing the effects of the cell cycle 10x |
Single Cell |
|
1H |
purlGTN:T00251 |
Hands-on |
Pre-processing of Single-Cell RNA Data
|
Single Cell |
|
3h |
purlGTN:T00241 |
Hands-on |
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution data management |
Single Cell |
|
1H |
purlGTN:T00336 |
Hands-on |
Inferring single cell trajectories (Monocle3, R) 10xpaper-replicationRrmarkdown-notebookjupyter-notebook |
Single Cell |
|
3H |
purlGTN:T00357 |
Hands-on |
Scanpy Parameter Iterator
|
Single Cell |
|
2H |
purlGTN:T00358 |
Hands-on |
Filter, plot and explore single-cell RNA-seq data (Scanpy, Python) 10xpaper-replicationPythonjupyter-notebook |
Single Cell |
|
3H |
purlGTN:T00245 |
Hands-on |
Generating a single cell matrix using Alevin 10xpaper-replication |
Single Cell |
|
2H |
purlGTN:T00240 |
Hands-on |
Bulk RNA Deconvolution with MuSiC transcriptomics |
Single Cell |
|
2h |
purlGTN:T00366 |
Hands-on |
Filter, plot, and explore single cell RNA-seq data (Seurat, R) 10xpaper-replicationRrmarkdown-notebookjupyter-notebook |
Single Cell |
|
3H |
purlGTN:T00247 |
Hands-on |
Filter, plot and explore single-cell RNA-seq data (Scanpy) 10xpaper-replication |
Single Cell |
|
3H |
purlGTN:T00374 |
Hands-on |
EBI Single Cell Expression Atlas files to AnnData (Scanpy) or Seurat Object | Creating preprocessed dataset for sc-RNA Filter, Plot, Explore tutorial data importdata management |
Single Cell |
|
15m |
purlGTN:T00371 |
Hands-on |
Asynchronous training
|
Teaching and Hosting Galaxy training |
|
1h |
purlGTN:T00283 |
Hands-on |
Organizing a workshop
|
Teaching and Hosting Galaxy training |
|
3H |
purlGTN:T00284 |
Hands-on |
Running a workshop as instructor
|
Teaching and Hosting Galaxy training |
|
3H |
purlGTN:T00282 |
Hands-on |
Motivation and Demotivation
|
Teaching and Hosting Galaxy training |
|
60m |
purlGTN:T00287 |
Hands-on |
Teaching online
|
Teaching and Hosting Galaxy training |
|
1h |
purlGTN:T00285 |
Hands-on |
Set up a Galaxy for Training
|
Teaching and Hosting Galaxy training |
|
2h |
purlGTN:T00286 |
Hands-on |
Training Infrastructure as a Service cyoa |
Teaching and Hosting Galaxy training |
|
10m |
purlGTN:T00279 |
Hands-on |
Hybrid training
|
Teaching and Hosting Galaxy training |
|
1h |
purlGTN:T00281 |
Hands-on |
Live Coding is a Skill
|
Teaching and Hosting Galaxy training |
|
1h |
purlGTN:T00372 |
Hands-on |
Course Builder cyoa |
Teaching and Hosting Galaxy training |
|
10m |
purlGTN:T00354 |
Hands-on |
Train-the-Trainer: putting it all together
|
Teaching and Hosting Galaxy training |
|
60m |
purlGTN:T00280 |
Hands-on |
Training techniques to enhance learner participation and engagement
|
Teaching and Hosting Galaxy training |
|
60m |
purlGTN:T00277 |
Hands-on |
Teaching experiences
|
Teaching and Hosting Galaxy training |
|
1h |
purlGTN:T00276 |
Hands-on |
Assessment and feedback in training and teachings
|
Teaching and Hosting Galaxy training |
|
3h30m |
purlGTN:T00278 |
Hands-on |
Galaxy Admin Training
|
Teaching and Hosting Galaxy training |
|
60m |
purlGTN:T00030 |
Hands-on |
Chloroplast genome assembly plantsnanopore |
Assembly |
|
2h |
purlGTN:T00038 |
Hands-on |
Unicycler Assembly prokaryotemicrogalaxy |
Assembly |
Introductory |
4h |
purlGTN:T00039 |
Hands-on |
VGP assembly pipeline pacbioeukaryoteVGP |
Assembly |
Intermediate |
5h |
purlGTN:T00036 |
Hands-on |
Genome Assembly of MRSA using Illumina MiSeq Data illuminaassemblyamrone-health |
Assembly |
|
2h |
purlGTN:T00029 |
Hands-on |
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads covid19 |
Assembly |
Intermediate |
4h |
purlGTN:T00331 |
Hands-on |
Large genome assembly and polishing assemblypolishingnanopore |
Assembly |
|
2h |
purlGTN:T00037 |
Hands-on |
Genome Assembly of MRSA using Oxford Nanopore MinION Data nanoporeassemblyamr |
Assembly |
|
2h |
purlGTN:T00032 |
Hands-on |
Making sense of a newly assembled genome prokaryotemicrogalaxy |
Assembly |
|
4h |
purlGTN:T00035 |
Hands-on |
Assembly of metagenomic sequencing data assemblymetagenomicsmicrogalaxy |
Assembly |
Introductory |
2H |
purlGTN:T00355 |
Hands-on |
ERGA post-assembly QC
|
Assembly |
|
3H |
purlGTN:T00031 |
Hands-on |
De Bruijn Graph Assembly
|
Assembly |
Introductory |
2h |
purlGTN:T00034 |
Hands-on |
An Introduction to Genome Assembly
|
Assembly |
Introductory |
30m |
purlGTN:T00040 |
Hands-on |
VGP assembly pipeline - short version pacbioeukaryoteVGP |
Assembly |
Intermediate |
1h |
purlGTN:T00028 |
Hands-on |
Genome Assembly Quality Control assemblyquality control |
Assembly |
Intermediate |
2h |
purlGTN:T00033 |
Hands-on |
Genome assembly using PacBio data assemblypacbio |
Assembly |
Intermediate |
6h |
purlGTN:T00293 |
Hands-on |
Network analysis with Heinz metatranscriptomicsnetwork analysis |
Transcriptomics |
|
1h30m |
purlGTN:T00289 |
Hands-on |
De novo transcriptome reconstruction with RNA-Seq
|
Transcriptomics |
|
6h |
purlGTN:T00303 |
Hands-on |
Visualization of RNA-Seq results with heatmap2
|
Transcriptomics |
|
1h |
purlGTN:T00291 |
Hands-on |
GO Enrichment Analysis
|
Transcriptomics |
|
1h |
purlGTN:T00304 |
Hands-on |
Visualization of RNA-Seq results with Volcano Plot
|
Transcriptomics |
Introductory |
30m |
purlGTN:T00302 |
Hands-on |
Visualization of RNA-Seq results with CummeRbund
|
Transcriptomics |
|
1h |
purlGTN:T00306 |
Hands-on |
Small Non-coding RNA Clustering using BlockClust
|
Transcriptomics |
|
1H |
purlGTN:T00299 |
Hands-on |
RNA Seq Counts to Viz in R interactive-tools |
Transcriptomics |
|
1H |
purlGTN:T00345 |
Hands-on |
Genome-wide alternative splicing analysis alternative splicingisoform switching |
Transcriptomics |
Advanced |
3H |
purlGTN:T00307 |
Hands-on |
Differential abundance testing of small RNAs
|
Transcriptomics |
|
3h |
purlGTN:T00305 |
Hands-on |
Visualization of RNA-Seq results with Volcano Plot in R interactive-tools |
Transcriptomics |
Intermediate |
1H |
purlGTN:T00300 |
Hands-on |
3: RNA-seq genes to pathways mouse |
Transcriptomics |
|
2h |
purlGTN:T00294 |
Hands-on |
Reference-based RNAseq data analysis (long)
|
Transcriptomics |
|
1h |
purlGTN:T00292 |
Hands-on |
Whole transcriptome analysis of Arabidopsis thaliana miRNAplantsstress tolerance |
Transcriptomics |
|
2H |
purlGTN:T00297 |
Hands-on |
RNA-Seq analysis with AskOmics Interactive Tool
|
Transcriptomics |
|
2H |
purlGTN:T00290 |
Hands-on |
De novo transcriptome assembly, annotation, and differential expression analysis
|
Transcriptomics |
|
3H |
purlGTN:T00298 |
Hands-on |
2: RNA-seq counts to genes limma-voommouseQC |
Transcriptomics |
|
2h |
purlGTN:T00295 |
Hands-on |
Reference-based RNA-Seq data analysis bulkrna-seqcollectionsdrosophilaQCcyoa |
Transcriptomics |
Introductory |
8h |
purlGTN:T00301 |
Hands-on |
1: RNA-Seq reads to counts collectionsmouseQC |
Transcriptomics |
|
3h |
purlGTN:T00296 |
Hands-on |
RNA-RNA interactome data analysis
|
Transcriptomics |
|
2H |
purlGTN:T00288 |
Hands-on |
CLIP-Seq data analysis from pre-processing to motif detection
|
Transcriptomics |
|
6h |
purlGTN:T00346 |
Hands-on |
RNA-seq Alignment with STAR
|
Transcriptomics |
|
90M |
purlGTN:T00153 |
Hands-on |
JupyterLab in Galaxy interactive-tools |
Using Galaxy and Managing your Data |
|
1H |
purlGTN:T00147 |
Hands-on |
Downloading and Deleting Data in Galaxy
|
Using Galaxy and Managing your Data |
Introductory |
20M |
purlGTN:T00159 |
Hands-on |
Submitting sequence data to ENA covid19 |
Using Galaxy and Managing your Data |
Intermediate |
1h |
purlGTN:T00148 |
Hands-on |
Use Jupyter notebooks in Galaxy
|
Using Galaxy and Managing your Data |
|
30m |
purlGTN:T00156 |
Hands-on |
Multisample Analysis collections |
Using Galaxy and Managing your Data |
Advanced |
1h |
purlGTN:T00160 |
Hands-on |
Rule Based Uploader collectionstags |
Using Galaxy and Managing your Data |
Intermediate |
20m |
purlGTN:T00151 |
Hands-on |
Extracting Workflows from Histories workflows |
Using Galaxy and Managing your Data |
|
30m |
purlGTN:T00164 |
Hands-on |
Using Workflow Parameters workflows |
Using Galaxy and Managing your Data |
Intermediate |
30m |
purlGTN:T00158 |
Hands-on |
Searching Your History
|
Using Galaxy and Managing your Data |
Introductory |
5m |
purlGTN:T00149 |
Hands-on |
Group tags for complex experimental designs
|
Using Galaxy and Managing your Data |
|
10m |
purlGTN:T00150 |
Hands-on |
Understanding Galaxy history system
|
Using Galaxy and Managing your Data |
|
30m |
purlGTN:T00152 |
Hands-on |
InterMine integration with Galaxy
|
Using Galaxy and Managing your Data |
|
1h |
purlGTN:T00162 |
Hands-on |
Automating Galaxy workflows using the command line workflowsvariant-analysiscovid19 |
Using Galaxy and Managing your Data |
|
2h |
purlGTN:T00165 |
Hands-on |
Workflow Reports workflows |
Using Galaxy and Managing your Data |
Intermediate |
30m |
purlGTN:T00146 |
Hands-on |
Using dataset collections collections |
Using Galaxy and Managing your Data |
Intermediate |
30m |
purlGTN:T00157 |
Hands-on |
RStudio in Galaxy interactive-tools |
Using Galaxy and Managing your Data |
|
3H |
purlGTN:T00161 |
Hands-on |
Rule Based Uploader: Advanced collectionstags |
Using Galaxy and Managing your Data |
Advanced |
20m |
purlGTN:T00155 |
Hands-on |
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis ncbicovid19 |
Using Galaxy and Managing your Data |
|
30m |
purlGTN:T00163 |
Hands-on |
Creating, Editing and Importing Galaxy Workflows workflows |
Using Galaxy and Managing your Data |
Intermediate |
30m |
purlGTN:T00154 |
Hands-on |
Name tags for following complex histories
|
Using Galaxy and Managing your Data |
|
20m |
purlGTN:T00258 |
Hands-on |
Deep Learning (Part 1) - Feedforward neural networks (FNN)
|
Statistics and machine learning |
|
2H |
purlGTN:T00260 |
Hands-on |
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis Machine learningPan-cancercancer biomarkersoncogenes and tumor suppressor genes |
Statistics and machine learning |
|
1H30M |
purlGTN:T00259 |
Hands-on |
Deep Learning (Part 2) - Recurrent neural networks (RNN)
|
Statistics and machine learning |
|
2H |
purlGTN:T00268 |
Hands-on |
Introduction to deep learning
|
Statistics and machine learning |
|
1H |
purlGTN:T00271 |
Hands-on |
Regression in Machine Learning
|
Statistics and machine learning |
|
2H |
purlGTN:T00337 |
Hands-on |
Supervised Learning with Hyperdimensional Computing
|
Statistics and machine learning |
Intermediate |
30m |
purlGTN:T00257 |
Hands-on |
Deep Learning (Part 3) - Convolutional neural networks (CNN)
|
Statistics and machine learning |
|
2H |
purlGTN:T00266 |
Hands-on |
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy interactive-toolsmachine-learningdeep-learningjupyter-labimage-segmentationprotein-3D-structure |
Statistics and machine learning |
|
1H |
purlGTN:T00262 |
Hands-on |
Classification in Machine Learning
|
Statistics and machine learning |
|
2H |
purlGTN:T00263 |
Hands-on |
Machine learning: classification and regression
|
Statistics and machine learning |
|
1H |
purlGTN:T00269 |
Hands-on |
Interval-Wise Testing for omics data
|
Statistics and machine learning |
|
1h |
purlGTN:T00272 |
Hands-on |
Text-mining with the SimText toolset interactive-tools |
Statistics and machine learning |
|
1H |
purlGTN:T00264 |
Hands-on |
Clustering in Machine Learning
|
Statistics and machine learning |
|
2H |
purlGTN:T00265 |
Hands-on |
Image classification in Galaxy with fruit 360 dataset
|
Statistics and machine learning |
|
2H |
purlGTN:T00267 |
Hands-on |
Introduction to Machine Learning using R interactive-tools |
Statistics and machine learning |
Intermediate |
3H |
purlGTN:T00270 |
Hands-on |
Basics of machine learning
|
Statistics and machine learning |
|
30M |
purlGTN:T00261 |
Hands-on |
Age prediction using machine learning
|
Statistics and machine learning |
|
2H |
purlGTN:T00167 |
Hands-on |
Genome annotation with Maker (short) eukaryote |
Genome Annotation |
Intermediate |
2h |
purlGTN:T00173 |
Hands-on |
Functional annotation of protein sequences eukaryote |
Genome Annotation |
Introductory |
1h |
purlGTN:T00176 |
Hands-on |
From small to large-scale genome comparison
|
Genome Annotation |
|
2H |
purlGTN:T00172 |
Hands-on |
Genome annotation with Funannotate eukaryote |
Genome Annotation |
Intermediate |
8h |
purlGTN:T00169 |
Hands-on |
Refining Genome Annotations with Apollo (prokaryotes) prokaryotemicrogalaxy |
Genome Annotation |
Intermediate |
3h |
purlGTN:T00178 |
Hands-on |
Masking repeats with RepeatMasker eukaryote |
Genome Annotation |
Introductory |
1H |
purlGTN:T00171 |
Hands-on |
CRISPR screen analysis genome editingCRISPRessential genescell line |
Genome Annotation |
|
2H |
purlGTN:T00179 |
Hands-on |
Essential genes detection with Transposon insertion sequencing bacteriatnseqessential genes |
Genome Annotation |
|
7H |
purlGTN:T00168 |
Hands-on |
Genome annotation with Prokka prokaryotemicrogalaxy |
Genome Annotation |
Introductory |
1h |
purlGTN:T00170 |
Hands-on |
Refining Genome Annotations with Apollo (eukaryotes) eukaryotecyoa |
Genome Annotation |
Intermediate |
3h |
purlGTN:T00177 |
Hands-on |
Long non-coding RNAs (lncRNAs) annotation with FEELnc eukaryote |
Genome Annotation |
Intermediate |
2h |
purlGTN:T00370 |
Hands-on |
Creating an Official Gene Set
|
Genome Annotation |
|
30M |
purlGTN:T00175 |
Hands-on |
Genome Annotation prokaryotework-in-progress |
Genome Annotation |
Introductory |
2H |
purlGTN:T00174 |
Hands-on |
Comparative gene analysis in unannotated genomes evolutionannotationvgpcookbookeukaryoteprokaryotemicrogalaxy |
Genome Annotation |
|
30M |
purlGTN:T00166 |
Hands-on |
Genome annotation with Maker eukaryote |
Genome Annotation |
Advanced |
4h |
purlGTN:T00198 |
Hands-on |
Mass spectrometry imaging: Examining the spatial distribution of analytes
|
Metabolomics |
Introductory |
1H |
purlGTN:T00199 |
Hands-on |
Mass spectrometry imaging: Finding differential analytes
|
Metabolomics |
Intermediate |
2H |
purlGTN:T00194 |
Hands-on |
Mass spectrometry : GC-MS analysis with metaMS package
|
Metabolomics |
Introductory |
2H |
purlGTN:T00196 |
Hands-on |
Mass spectrometry: LC-MS data processing
|
Metabolomics |
Introductory |
2H |
purlGTN:T00197 |
Hands-on |
Mass spectrometry: LC-MS preprocessing with XCMS
|
Metabolomics |
Intermediate |
3h |
purlGTN:T00195 |
Hands-on |
Mass spectrometry: LC-MS analysis
|
Metabolomics |
|
3h |
purlGTN:T00344 |
Hands-on |
Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
|
Metabolomics |
Intermediate |
2H |
purlGTN:F00240 |
FAQs |
How can I create a tutorial skeleton from a Galaxy workflow?
|
Contributing to the Galaxy Training Material |
|
|
purlGTN:F00110 |
FAQs |
Using tutorial mode
|
|
|
|
purlGTN:F00220 |
FAQs |
I got slightly different numbers than were in the tutorial
|
Introduction to Galaxy Analyses |
|
|
purlGTN:F00258 |
FAQs |
UCSC import: what should my file look like?
|
Epigenetics |
|
|
purlGTN:F00326 |
FAQs |
The UMAP Plots errors out sometimes?
|
Single Cell |
|
|
purlGTN:F00229 |
FAQs |
Are UMIs not actually unique?
|
Single Cell |
|
|
purlGTN:F00235 |
FAQs |
Downloading the files from the NCBI server fails or takes too long.
|
Assembly |
|
|
purlGTN:F00354 |
FAQs |
How can I talk with other users?
|
Single Cell |
|
|
purlGTN:F00111 |
FAQs |
Does your account usage quota seem incorrect?
|
|
|
|
purlGTN:F00112 |
FAQs |
Forgot Password
|
|
|
|
purlGTN:F00113 |
FAQs |
Changing acount email or password
|
|
|
|
purlGTN:F00230 |
FAQs |
Why do we only consider highly variable genes?
|
Single Cell |
|
|
purlGTN:F00347 |
FAQs |
Can we use snippy pipeline instead for the phylogenetic analysis?
|
Metagenomics |
|
|
purlGTN:F00312 |
FAQs |
Why do we have a variant mapping file when it is not being used in the workflow?
|
Proteomics |
|
|
purlGTN:F00114 |
FAQs |
Using IGV with Galaxy
|
|
|
|
purlGTN:F00231 |
FAQs |
Add genome and annotations to IGV from Galaxy
|
Visualisation |
|
|
purlGTN:F00232 |
FAQs |
Add Mapped reads track to IGV from Galaxy
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Visualisation |
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purlGTN:F00270 |
FAQs |
Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
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Metagenomics |
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purlGTN:F00356 |
FAQs |
What is a Learning Pathway?
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purlGTN:F00181 |
FAQs |
Why host your materials with the GTN?
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purlGTN:F00115 |
FAQs |
Why not use Excel?
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purlGTN:F00281 |
FAQs |
Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?
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Proteomics |
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purlGTN:F00348 |
FAQs |
Can we also use this workflow on Illumina raw reads?
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Metagenomics |
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purlGTN:F00349 |
FAQs |
Do the pipelines work with both isolates and direct from raw meat? or only isolate?
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Metagenomics |
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purlGTN:F00116 |
FAQs |
Annotate a workflow
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purlGTN:F00117 |
FAQs |
Creating a new workflow
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purlGTN:F00118 |
FAQs |
Opening the workflow editor
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purlGTN:F00119 |
FAQs |
Extracting a workflow from your history
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purlGTN:F00136 |
FAQs |
Extraer un flujo de trabajo de tu historial
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purlGTN:F00120 |
FAQs |
Hiding intermediate steps
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purlGTN:F00121 |
FAQs |
Importing a workflow
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purlGTN:F00175 |
FAQs |
Import workflows from WorkflowHub
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purlGTN:F00122 |
FAQs |
Importing a workflow using the search
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purlGTN:F00123 |
FAQs |
Setting parameters at run-time
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purlGTN:F00124 |
FAQs |
Make a workflow public
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purlGTN:F00125 |
FAQs |
Renaming workflow outputs
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purlGTN:F00126 |
FAQs |
Viewing a workflow report
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purlGTN:F00127 |
FAQs |
Running a workflow
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purlGTN:F00176 |
FAQs |
Importing and Launching a workflow
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